diff --git a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.csl b/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.csl
deleted file mode 100644
index dd1d41c..0000000
--- a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.csl
+++ /dev/null
@@ -1,2 +0,0 @@
-// once a station becomes full, probability it will be polled within T time units is ...
-P=?[ true U<=10 (s=1 & a=0) ]
\ No newline at end of file
diff --git a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.prism b/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.prism
deleted file mode 100644
index d1db524..0000000
--- a/Benchmarks/PRISM/Polling/Polling_N_12/polling_T_10_N_12.prism
+++ /dev/null
@@ -1,90 +0,0 @@
-// polling example [IT90]
-// gxn/dxp 26/01/00
-
-ctmc
-
-const int N = 12;
-
-const double mu		= 1;
-const double gamma	= 200;
-const double lambda	= mu/N;
-
-module server
-	
-	s : [1..N]; // station
-	a : [0..1]; // action: 0=polling, 1=serving
-	
-	[loop1a] (s=1)&(a=0) -> gamma	: (s'=s+1);
-	[loop1b] (s=1)&(a=0) -> gamma	: (a'=1);
-	[serve1] (s=1)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop2a] (s=2)&(a=0) -> gamma	: (s'=s+1);
-	[loop2b] (s=2)&(a=0) -> gamma	: (a'=1);
-	[serve2] (s=2)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop3a] (s=3)&(a=0) -> gamma	: (s'=s+1);
-	[loop3b] (s=3)&(a=0) -> gamma	: (a'=1);
-	[serve3] (s=3)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop4a] (s=4)&(a=0) -> gamma	: (s'=s+1);
-	[loop4b] (s=4)&(a=0) -> gamma	: (a'=1);
-	[serve4] (s=4)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop5a] (s=5)&(a=0) -> gamma	: (s'=s+1);
-	[loop5b] (s=5)&(a=0) -> gamma	: (a'=1);
-	[serve5] (s=5)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop6a] (s=6)&(a=0) -> gamma	: (s'=s+1);
-	[loop6b] (s=6)&(a=0) -> gamma	: (a'=1);
-	[serve6] (s=6)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop7a] (s=7)&(a=0) -> gamma	: (s'=s+1);
-	[loop7b] (s=7)&(a=0) -> gamma	: (a'=1);
-	[serve7] (s=7)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop8a] (s=8)&(a=0) -> gamma	: (s'=s+1);
-	[loop8b] (s=8)&(a=0) -> gamma	: (a'=1);
-	[serve8] (s=8)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop9a] (s=9)&(a=0) -> gamma	: (s'=s+1);
-	[loop9b] (s=9)&(a=0) -> gamma	: (a'=1);
-	[serve9] (s=9)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop10a] (s=10)&(a=0) -> gamma	: (s'=s+1);
-	[loop10b] (s=10)&(a=0) -> gamma	: (a'=1);
-	[serve10] (s=10)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop11a] (s=11)&(a=0) -> gamma	: (s'=s+1);
-	[loop11b] (s=11)&(a=0) -> gamma	: (a'=1);
-	[serve11] (s=11)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop12a] (s=12)&(a=0) -> gamma	: (s'=1);
-	[loop12b] (s=12)&(a=0) -> gamma	: (a'=1);
-	[serve12] (s=12)&(a=1) -> mu		: (s'=1)&(a'=0);
-	
-endmodule
-
-module station1
-	
-	s1 : [0..1]; // state of station: 0=empty, 1=full
-	
-	[loop1a] (s1=0) -> 1 : (s1'=0);
-	[]       (s1=0) -> lambda : (s1'=1);
-	[loop1b] (s1=1) -> 1 : (s1'=1);
-	[serve1] (s1=1) -> 1 : (s1'=0);
-	
-endmodule
-
-// construct further stations through renaming
-
-module station2 = station1 [ s1=s2, loop1a=loop2a, loop1b=loop2b, serve1=serve2 ] endmodule
-module station3 = station1 [ s1=s3, loop1a=loop3a, loop1b=loop3b, serve1=serve3 ] endmodule
-module station4 = station1 [ s1=s4, loop1a=loop4a, loop1b=loop4b, serve1=serve4 ] endmodule
-module station5 = station1 [ s1=s5, loop1a=loop5a, loop1b=loop5b, serve1=serve5 ] endmodule
-module station6 = station1 [ s1=s6, loop1a=loop6a, loop1b=loop6b, serve1=serve6 ] endmodule
-module station7 = station1 [ s1=s7, loop1a=loop7a, loop1b=loop7b, serve1=serve7 ] endmodule
-module station8 = station1 [ s1=s8, loop1a=loop8a, loop1b=loop8b, serve1=serve8 ] endmodule
-module station9 = station1 [ s1=s9, loop1a=loop9a, loop1b=loop9b, serve1=serve9 ] endmodule
-module station10 = station1 [ s1=s10, loop1a=loop10a, loop1b=loop10b, serve1=serve10 ] endmodule
-module station11 = station1 [ s1=s11, loop1a=loop11a, loop1b=loop11b, serve1=serve11 ] endmodule
-module station12 = station1 [ s1=s12, loop1a=loop12a, loop1b=loop12b, serve1=serve12 ] endmodule
diff --git a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.csl b/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.csl
deleted file mode 100644
index dd1d41c..0000000
--- a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.csl
+++ /dev/null
@@ -1,2 +0,0 @@
-// once a station becomes full, probability it will be polled within T time units is ...
-P=?[ true U<=10 (s=1 & a=0) ]
\ No newline at end of file
diff --git a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.prism b/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.prism
deleted file mode 100644
index 7abe195..0000000
--- a/Benchmarks/PRISM/Polling/Polling_N_16/polling_T_10_N_16.prism
+++ /dev/null
@@ -1,110 +0,0 @@
-// polling example [IT90]
-// gxn/dxp 26/01/00
-
-ctmc
-
-const int N = 16;
-
-const double mu		= 1;
-const double gamma	= 200;
-const double lambda	= mu/N;
-
-module server
-	
-	s : [1..N]; // station
-	a : [0..1]; // action: 0=polling, 1=serving
-	
-	[loop1a] (s=1)&(a=0) -> gamma	: (s'=s+1);
-	[loop1b] (s=1)&(a=0) -> gamma	: (a'=1);
-	[serve1] (s=1)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop2a] (s=2)&(a=0) -> gamma	: (s'=s+1);
-	[loop2b] (s=2)&(a=0) -> gamma	: (a'=1);
-	[serve2] (s=2)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop3a] (s=3)&(a=0) -> gamma	: (s'=s+1);
-	[loop3b] (s=3)&(a=0) -> gamma	: (a'=1);
-	[serve3] (s=3)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop4a] (s=4)&(a=0) -> gamma	: (s'=s+1);
-	[loop4b] (s=4)&(a=0) -> gamma	: (a'=1);
-	[serve4] (s=4)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop5a] (s=5)&(a=0) -> gamma	: (s'=s+1);
-	[loop5b] (s=5)&(a=0) -> gamma	: (a'=1);
-	[serve5] (s=5)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop6a] (s=6)&(a=0) -> gamma	: (s'=s+1);
-	[loop6b] (s=6)&(a=0) -> gamma	: (a'=1);
-	[serve6] (s=6)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop7a] (s=7)&(a=0) -> gamma	: (s'=s+1);
-	[loop7b] (s=7)&(a=0) -> gamma	: (a'=1);
-	[serve7] (s=7)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop8a] (s=8)&(a=0) -> gamma	: (s'=s+1);
-	[loop8b] (s=8)&(a=0) -> gamma	: (a'=1);
-	[serve8] (s=8)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop9a] (s=9)&(a=0) -> gamma	: (s'=s+1);
-	[loop9b] (s=9)&(a=0) -> gamma	: (a'=1);
-	[serve9] (s=9)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop10a] (s=10)&(a=0) -> gamma	: (s'=s+1);
-	[loop10b] (s=10)&(a=0) -> gamma	: (a'=1);
-	[serve10] (s=10)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop11a] (s=11)&(a=0) -> gamma	: (s'=s+1);
-	[loop11b] (s=11)&(a=0) -> gamma	: (a'=1);
-	[serve11] (s=11)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop12a] (s=12)&(a=0) -> gamma	: (s'=s+1);
-	[loop12b] (s=12)&(a=0) -> gamma	: (a'=1);
-	[serve12] (s=12)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop13a] (s=13)&(a=0) -> gamma	: (s'=s+1);
-	[loop13b] (s=13)&(a=0) -> gamma	: (a'=1);
-	[serve13] (s=13)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop14a] (s=14)&(a=0) -> gamma	: (s'=s+1);
-	[loop14b] (s=14)&(a=0) -> gamma	: (a'=1);
-	[serve14] (s=14)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop15a] (s=15)&(a=0) -> gamma	: (s'=s+1);
-	[loop15b] (s=15)&(a=0) -> gamma	: (a'=1);
-	[serve15] (s=15)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop16a] (s=16)&(a=0) -> gamma	: (s'=1);
-	[loop16b] (s=16)&(a=0) -> gamma	: (a'=1);
-	[serve16] (s=16)&(a=1) -> mu		: (s'=1)&(a'=0);
-	
-endmodule
-
-module station1
-	
-	s1 : [0..1]; // state of station: 0=empty, 1=full
-	
-	[loop1a] (s1=0) -> 1 : (s1'=0);
-	[]       (s1=0) -> lambda : (s1'=1);
-	[loop1b] (s1=1) -> 1 : (s1'=1);
-	[serve1] (s1=1) -> 1 : (s1'=0);
-	
-endmodule
-
-// construct further stations through renaming
-
-module station2 = station1 [ s1=s2, loop1a=loop2a, loop1b=loop2b, serve1=serve2 ] endmodule
-module station3 = station1 [ s1=s3, loop1a=loop3a, loop1b=loop3b, serve1=serve3 ] endmodule
-module station4 = station1 [ s1=s4, loop1a=loop4a, loop1b=loop4b, serve1=serve4 ] endmodule
-module station5 = station1 [ s1=s5, loop1a=loop5a, loop1b=loop5b, serve1=serve5 ] endmodule
-module station6 = station1 [ s1=s6, loop1a=loop6a, loop1b=loop6b, serve1=serve6 ] endmodule
-module station7 = station1 [ s1=s7, loop1a=loop7a, loop1b=loop7b, serve1=serve7 ] endmodule
-module station8 = station1 [ s1=s8, loop1a=loop8a, loop1b=loop8b, serve1=serve8 ] endmodule
-module station9 = station1 [ s1=s9, loop1a=loop9a, loop1b=loop9b, serve1=serve9 ] endmodule
-module station10 = station1 [ s1=s10, loop1a=loop10a, loop1b=loop10b, serve1=serve10 ] endmodule
-module station11 = station1 [ s1=s11, loop1a=loop11a, loop1b=loop11b, serve1=serve11 ] endmodule
-module station12 = station1 [ s1=s12, loop1a=loop12a, loop1b=loop12b, serve1=serve12 ] endmodule
-module station13 = station1 [ s1=s13, loop1a=loop13a, loop1b=loop13b, serve1=serve13 ] endmodule
-module station14 = station1 [ s1=s14, loop1a=loop14a, loop1b=loop14b, serve1=serve14 ] endmodule
-module station15 = station1 [ s1=s15, loop1a=loop15a, loop1b=loop15b, serve1=serve15 ] endmodule
-module station16 = station1 [ s1=s16, loop1a=loop16a, loop1b=loop16b, serve1=serve16 ] endmodule
diff --git a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.csl b/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.csl
deleted file mode 100644
index dd1d41c..0000000
--- a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.csl
+++ /dev/null
@@ -1,2 +0,0 @@
-// once a station becomes full, probability it will be polled within T time units is ...
-P=?[ true U<=10 (s=1 & a=0) ]
\ No newline at end of file
diff --git a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.prism b/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.prism
deleted file mode 100644
index bee0591..0000000
--- a/Benchmarks/PRISM/Polling/Polling_N_20/polling_T_10_N_20.prism
+++ /dev/null
@@ -1,130 +0,0 @@
-// polling example [IT90]
-// gxn/dxp 26/01/00
-
-ctmc
-
-const int N = 20;
-
-const double mu		= 1;
-const double gamma	= 200;
-const double lambda	= mu/N;
-
-module server
-	
-	s : [1..N]; // station
-	a : [0..1]; // action: 0=polling, 1=serving
-	
-	[loop1a] (s=1)&(a=0) -> gamma	: (s'=s+1);
-	[loop1b] (s=1)&(a=0) -> gamma	: (a'=1);
-	[serve1] (s=1)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop2a] (s=2)&(a=0) -> gamma	: (s'=s+1);
-	[loop2b] (s=2)&(a=0) -> gamma	: (a'=1);
-	[serve2] (s=2)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop3a] (s=3)&(a=0) -> gamma	: (s'=s+1);
-	[loop3b] (s=3)&(a=0) -> gamma	: (a'=1);
-	[serve3] (s=3)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop4a] (s=4)&(a=0) -> gamma	: (s'=s+1);
-	[loop4b] (s=4)&(a=0) -> gamma	: (a'=1);
-	[serve4] (s=4)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop5a] (s=5)&(a=0) -> gamma	: (s'=s+1);
-	[loop5b] (s=5)&(a=0) -> gamma	: (a'=1);
-	[serve5] (s=5)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop6a] (s=6)&(a=0) -> gamma	: (s'=s+1);
-	[loop6b] (s=6)&(a=0) -> gamma	: (a'=1);
-	[serve6] (s=6)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop7a] (s=7)&(a=0) -> gamma	: (s'=s+1);
-	[loop7b] (s=7)&(a=0) -> gamma	: (a'=1);
-	[serve7] (s=7)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop8a] (s=8)&(a=0) -> gamma	: (s'=s+1);
-	[loop8b] (s=8)&(a=0) -> gamma	: (a'=1);
-	[serve8] (s=8)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop9a] (s=9)&(a=0) -> gamma	: (s'=s+1);
-	[loop9b] (s=9)&(a=0) -> gamma	: (a'=1);
-	[serve9] (s=9)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop10a] (s=10)&(a=0) -> gamma	: (s'=s+1);
-	[loop10b] (s=10)&(a=0) -> gamma	: (a'=1);
-	[serve10] (s=10)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop11a] (s=11)&(a=0) -> gamma	: (s'=s+1);
-	[loop11b] (s=11)&(a=0) -> gamma	: (a'=1);
-	[serve11] (s=11)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop12a] (s=12)&(a=0) -> gamma	: (s'=s+1);
-	[loop12b] (s=12)&(a=0) -> gamma	: (a'=1);
-	[serve12] (s=12)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop13a] (s=13)&(a=0) -> gamma	: (s'=s+1);
-	[loop13b] (s=13)&(a=0) -> gamma	: (a'=1);
-	[serve13] (s=13)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop14a] (s=14)&(a=0) -> gamma	: (s'=s+1);
-	[loop14b] (s=14)&(a=0) -> gamma	: (a'=1);
-	[serve14] (s=14)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop15a] (s=15)&(a=0) -> gamma	: (s'=s+1);
-	[loop15b] (s=15)&(a=0) -> gamma	: (a'=1);
-	[serve15] (s=15)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop16a] (s=16)&(a=0) -> gamma	: (s'=s+1);
-	[loop16b] (s=16)&(a=0) -> gamma	: (a'=1);
-	[serve16] (s=16)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop17a] (s=17)&(a=0) -> gamma	: (s'=s+1);
-	[loop17b] (s=17)&(a=0) -> gamma	: (a'=1);
-	[serve17] (s=17)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop18a] (s=18)&(a=0) -> gamma	: (s'=s+1);
-	[loop18b] (s=18)&(a=0) -> gamma	: (a'=1);
-	[serve18] (s=18)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop19a] (s=19)&(a=0) -> gamma	: (s'=s+1);
-	[loop19b] (s=19)&(a=0) -> gamma	: (a'=1);
-	[serve19] (s=19)&(a=1) -> mu		: (s'=s+1)&(a'=0);
-	
-	[loop20a] (s=20)&(a=0) -> gamma	: (s'=1);
-	[loop20b] (s=20)&(a=0) -> gamma	: (a'=1);
-	[serve20] (s=20)&(a=1) -> mu		: (s'=1)&(a'=0);
-	
-endmodule
-
-module station1
-	
-	s1 : [0..1]; // state of station: 0=empty, 1=full
-	
-	[loop1a] (s1=0) -> 1 : (s1'=0);
-	[]       (s1=0) -> lambda : (s1'=1);
-	[loop1b] (s1=1) -> 1 : (s1'=1);
-	[serve1] (s1=1) -> 1 : (s1'=0);
-	
-endmodule
-
-// construct further stations through renaming
-
-module station2 = station1 [ s1=s2, loop1a=loop2a, loop1b=loop2b, serve1=serve2 ] endmodule
-module station3 = station1 [ s1=s3, loop1a=loop3a, loop1b=loop3b, serve1=serve3 ] endmodule
-module station4 = station1 [ s1=s4, loop1a=loop4a, loop1b=loop4b, serve1=serve4 ] endmodule
-module station5 = station1 [ s1=s5, loop1a=loop5a, loop1b=loop5b, serve1=serve5 ] endmodule
-module station6 = station1 [ s1=s6, loop1a=loop6a, loop1b=loop6b, serve1=serve6 ] endmodule
-module station7 = station1 [ s1=s7, loop1a=loop7a, loop1b=loop7b, serve1=serve7 ] endmodule
-module station8 = station1 [ s1=s8, loop1a=loop8a, loop1b=loop8b, serve1=serve8 ] endmodule
-module station9 = station1 [ s1=s9, loop1a=loop9a, loop1b=loop9b, serve1=serve9 ] endmodule
-module station10 = station1 [ s1=s10, loop1a=loop10a, loop1b=loop10b, serve1=serve10 ] endmodule
-module station11 = station1 [ s1=s11, loop1a=loop11a, loop1b=loop11b, serve1=serve11 ] endmodule
-module station12 = station1 [ s1=s12, loop1a=loop12a, loop1b=loop12b, serve1=serve12 ] endmodule
-module station13 = station1 [ s1=s13, loop1a=loop13a, loop1b=loop13b, serve1=serve13 ] endmodule
-module station14 = station1 [ s1=s14, loop1a=loop14a, loop1b=loop14b, serve1=serve14 ] endmodule
-module station15 = station1 [ s1=s15, loop1a=loop15a, loop1b=loop15b, serve1=serve15 ] endmodule
-module station16 = station1 [ s1=s16, loop1a=loop16a, loop1b=loop16b, serve1=serve16 ] endmodule
-module station17 = station1 [ s1=s17, loop1a=loop17a, loop1b=loop17b, serve1=serve17 ] endmodule
-module station18 = station1 [ s1=s18, loop1a=loop18a, loop1b=loop18b, serve1=serve18 ] endmodule
-module station19 = station1 [ s1=s19, loop1a=loop19a, loop1b=loop19b, serve1=serve19 ] endmodule
-module station20 = station1 [ s1=s20, loop1a=loop20a, loop1b=loop20b, serve1=serve20 ] endmodule
diff --git a/Benchmarks/PRISM/README.md b/Benchmarks/PRISM/README.md
deleted file mode 100644
index 9c1f3e3..0000000
--- a/Benchmarks/PRISM/README.md
+++ /dev/null
@@ -1,20 +0,0 @@
-# PRISM Benchmarks
-
-Some benchmarks here were taken from those provided by [PRISM](https://prismmodelchecker.org). The upstream URL is [https://github.com/prismmodelchecker/prism-benchmarks](https://github.com/prismmodelchecker/prism-benchmarks).
-
-## Jackson
-
-TODO: Steal description from PRISM folks
-
-## Polling
-
-TODO: Steal description from PRISM folks
-
-## Robot World
-
-TODO: Steal description from PRISM folks
-
-## Tandem Queue
-
-TODO: Steal description from PRISM folks
-
diff --git a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props
index 9662c48..3cc4dd8 100644
--- a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00001/00001-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm
index 0cd09ca..fa96c67 100644
--- a/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2bound.sm
similarity index 53%
rename from Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.sm
rename to Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2bound.sm
index 0ed4f14..82ab99a 100644
--- a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00001/00001-sbml-l3v2bound.sm
@@ -1,22 +1,25 @@
 // File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00023/00023-sbml-l3v2.xml
+// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00001/00001-sbml-l3v2.xml
 // @GeneticLogicLab
 
 ctmc
 
+const int MAX_AMOUNT = 200;
+
 // Compartment size
 
 // Model parameters
-const double Alpha = 1000.0; // 
-const double Mu = 0.1; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
+const int _X_MAX = MAX_AMOUNT;
 module _X
 
-  _X  :  int init 0;
+    _X : [0.._X_MAX] init 100;
 
-		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
+		// Birth
+		[Birth] _X <= _X_MAX-10 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -25,10 +28,10 @@ endmodule
 // Reaction rates
 module reaction_rates
 
-		// Immigration:  ->   -> _X
-		[Immigration] Alpha > 0 -> Alpha : true;
+		// Birth:  ->  _X -> _X
+		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00001/results.txt b/Benchmarks/SBMLstochasticTests/00001/results.txt
new file mode 100644
index 0000000..b0a9d89
--- /dev/null
+++ b/Benchmarks/SBMLstochasticTests/00001/results.txt
@@ -0,0 +1,2 @@
+0.6725212076689461
+0.6732478300215641
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props
index 8fb482f..7c139c3 100644
--- a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00002/00002-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm
index 03be53e..7a65479 100644
--- a/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00002/00002-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model local parameters
-const double local_Lambda_0 = 0.1; // 
-const double local_Mu_1 = 0.11; // 
+const double local_Lambda_0 = 0.1; //
+const double local_Mu_1 = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (local_Lambda_0 * _X) > 0 -> (local_Lambda_0 * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (local_Mu_1 * _X) > 0 -> (local_Mu_1 * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props
index a7584e6..3a0c431 100644
--- a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00003/00003-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 0.67379) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 0.67379) ]
diff --git a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm
index b3fe59d..83364bf 100644
--- a/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00003/00003-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 1.0; // 
-const double Mu = 1.1; // 
+const double Lambda = 1.0; //
+const double Mu = 1.1; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props
index 30b1078..83667e4 100644
--- a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00004/00004-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 6.06531) ]
\ No newline at end of file
+P=? [true U[0,50] (_X < 6.06531) ]
diff --git a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm
index 763c39e..b01e4a7 100644
--- a/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.sm
@@ -1,5 +1,5 @@
 // File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00004/00004-sbml-l3v2.xml
+// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBMLstochasticTests/00004/00004-sbml-l3v2.xml
 // @GeneticLogicLab
 
 ctmc
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 10;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -25,10 +25,10 @@ endmodule
 // Reaction rates
 module reaction_rates
 
-		// Birth:  ->  _X -> _X
+		// Birth: _X -> _X // 2
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death: _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00004/results.txt b/Benchmarks/SBMLstochasticTests/00004/results.txt
new file mode 100644
index 0000000..0c72a40
--- /dev/null
+++ b/Benchmarks/SBMLstochasticTests/00004/results.txt
@@ -0,0 +1,2 @@
+0.8511625487681788
+0.8515501349900346
diff --git a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props
index 84d3d24..ae1dc31 100644
--- a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00005/00005-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 6065.307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 6065.307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm
index a50e6be..d7baaeb 100644
--- a/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00005/00005-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 10000;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00005/results.txt b/Benchmarks/SBMLstochasticTests/00005/results.txt
new file mode 100644
index 0000000..61aabea
--- /dev/null
+++ b/Benchmarks/SBMLstochasticTests/00005/results.txt
@@ -0,0 +1,2 @@
+0.0
+0.9999999999999412
diff --git a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props
index 7bae58e..0695513 100644
--- a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00006/00006-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm
index 4875077..f2912df 100644
--- a/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00006/00006-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module Sink
   Sink  :  int init 0;
 
 		// Death
-		[Death] Sink > 0 -> (Sink' = Sink + 1);
+		[Death] Sink >= 0 -> (Sink' = Sink + 1);
 
 endmodule
 
diff --git a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props
index 8116f74..ce97fa1 100644
--- a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00007/00007-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm
index 3f31f1b..cdd4b47 100644
--- a/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00007/00007-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module Sink
   Sink  :  int init 0;
 
 		// Death
-		[Death] Sink > 0 -> (Sink' = Sink + 1);
+		[Death] Sink >= 0 -> (Sink' = Sink + 1);
 
 endmodule
 
diff --git a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props
index 3f2f2b5..ef2e2d3 100644
--- a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00008/00008-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm
index ad47519..bda5c68 100644
--- a/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00008/00008-sbml-l3v2.sm
@@ -8,8 +8,8 @@ ctmc
 const double Cell = 1.0;
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -17,7 +17,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -29,7 +29,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props
index 0e7a2a7..05c8ba7 100644
--- a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00009/00009-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm
index d470225..bc01e2d 100644
--- a/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00009/00009-sbml-l3v2.sm
@@ -8,8 +8,8 @@ ctmc
 const double Cell = 2.0;
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -17,7 +17,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -29,7 +29,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props
index a4cd534..c5d154d 100644
--- a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00010/00010-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm
index e644b67..e6a8b70 100644
--- a/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00010/00010-sbml-l3v2.sm
@@ -8,8 +8,8 @@ ctmc
 const double Cell = 1.0;
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -17,7 +17,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -29,7 +29,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props
index 6b42849..b50a47f 100644
--- a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00011/00011-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 77.88008) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X <= 20) ]
diff --git a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm
index 4700709..32dfaed 100644
--- a/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00011/00011-sbml-l3v2.sm
@@ -8,8 +8,8 @@ ctmc
 const double Cell = 2.0;
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -17,7 +17,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -29,7 +29,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props
index 04a649c..331d92a 100644
--- a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00012/00012-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm
index c681204..362693b 100644
--- a/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00012/00012-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X* 0.5 * 2) > 0 -> (Lambda * _X* 0.5 * 2) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props
index 70fb0f1..81bc885 100644
--- a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00013/00013-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm
index 1dad711..9a1fdfe 100644
--- a/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00013/00013-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.2; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.2; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X* 0.5) > 0 -> (Lambda * _X* 0.5) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props
index 3da903c..9e03f4a 100644
--- a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00014/00014-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm
index 943151a..47e3739 100644
--- a/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00014/00014-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (((Lambda * _X) / 2) / 0.5) > 0 -> (((Lambda * _X) / 2) / 0.5) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props
index 83f34b8..e0caad0 100644
--- a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00015/00015-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm
index 4226cd3..fe6bf66 100644
--- a/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00015/00015-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] ((Lambda * ( _X/ 2)) / 0.5) > 0 -> ((Lambda * ( _X/ 2)) / 0.5) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props
index 497063c..f5bdb17 100644
--- a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00016/00016-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm
index 0c79e66..c7f06e0 100644
--- a/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00016/00016-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] ((Lambda * _X) / (2 / 2)) > 0 -> ((Lambda * _X) / (2 / 2)) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props
index 7ce43b8..68b7ce6 100644
--- a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00017/00017-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm
index d0f37c5..28db085 100644
--- a/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00017/00017-sbml-l3v2.sm
@@ -8,8 +8,8 @@ ctmc
 const double Cell = 1.0;
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -17,7 +17,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -29,7 +29,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Cell * Lambda * _X) > 0 -> (Cell * Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Cell * Mu * _X) > 0 -> (Cell * Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props
index d30c4ca..465e9c3 100644
--- a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00018/00018-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 77.88008) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 77.88008) ]
diff --git a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm
index 25e19d0..57a8600 100644
--- a/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00018/00018-sbml-l3v2.sm
@@ -8,8 +8,8 @@ ctmc
 const double Cell = 0.5;
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -17,7 +17,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -29,7 +29,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Cell * Lambda * _X) > 0 -> (Cell * Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Cell * Mu * _X) > 0 -> (Cell * Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props
index 70ad67d..3e678f6 100644
--- a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00019/00019-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 60.65307) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 60.65307) ]
diff --git a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm
index 3122cb9..f34ff10 100644
--- a/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00019/00019-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Lambda = 0.1; // 
-const double Mu = 0.11; // 
+const double Lambda = 0.1; //
+const double Mu = 0.11; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 100;
 
 		// Birth
-		[Birth] _X > 0 -> (_X' = _X + 1);
+		[Birth] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -36,7 +36,7 @@ module reaction_rates
 		// Birth:  ->  _X -> _X
 		[Birth] (Lambda * _X) > 0 -> (Lambda * _X) : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props
index 76ed6d5..ea20172 100644
--- a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00020/00020-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 9.93262) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X > 9.93262) ]
diff --git a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm
index 22d2dad..c4e3cea 100644
--- a/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00020/00020-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 1.0; // 
-const double Mu = 0.1; // 
+const double Alpha = 1.0; //
+const double Mu = 0.1; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
+		[Immigration] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Immigration:  ->   -> _X
 		[Immigration] Alpha > 0 -> Alpha : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props
index 035426b..02b0248 100644
--- a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00021/00021-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 99.3262) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X > 99.3262) ]
diff --git a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm
index 90457ef..2bf7229 100644
--- a/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00021/00021-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 10.0; // 
-const double Mu = 0.1; // 
+const double Alpha = 10.0; //
+const double Mu = 0.1; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
+		[Immigration] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Immigration:  ->   -> _X
 		[Immigration] Alpha > 0 -> Alpha : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00021/results.txt b/Benchmarks/SBMLstochasticTests/00021/results.txt
new file mode 100644
index 0000000..b2dc1ea
--- /dev/null
+++ b/Benchmarks/SBMLstochasticTests/00021/results.txt
@@ -0,0 +1,2 @@
+0.0
+0.0
diff --git a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props
index 4c66ad6..d828aa1 100644
--- a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00022/00022-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 49.6631) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X > 49.6631) ]
diff --git a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm
index 9b8ebc7..b140861 100644
--- a/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00022/00022-sbml-l3v2.sm
@@ -7,11 +7,11 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 10.0; // 
-const double Mu = 0.1; // 
+const double Alpha = 10.0; //
+const double Mu = 0.1; //
 
 // Model local parameters
-const double local_Alpha_0 = 5.0; // 
+const double local_Alpha_0 = 5.0; //
 
 // Species _X
 module _X
@@ -19,7 +19,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
+		[Immigration] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -31,7 +31,7 @@ module reaction_rates
 		// Immigration:  ->   -> _X
 		[Immigration] local_Alpha_0 > 0 -> local_Alpha_0 : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.props
deleted file mode 100644
index d40963b..0000000
--- a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00023/00023-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X > 9932.62) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.xml
deleted file mode 100755
index 89af29b..0000000
--- a/Benchmarks/SBMLstochasticTests/00023/00023-sbml-l3v2.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="ImmigrationDeath04" name="Immigration-Death (002), variant 04" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="Alpha" value="1000" constant="true"/>
-      <parameter id="Mu" value="0.1" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Immigration" reversible="false">
-        <listOfProducts>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <ci> Alpha </ci>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Death" reversible="false">
-        <listOfReactants>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> Mu </ci>
-              <ci> X </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.props
deleted file mode 100644
index 3c6ef61..0000000
--- a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00024/00024-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X > 99.3262) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.sm
deleted file mode 100644
index 90b352e..0000000
--- a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.sm
+++ /dev/null
@@ -1,62 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00024/00024-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-
-// Model parameters
-const double Alpha = 10.0; // 
-const double Mu = 0.1; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
-		// Death
-		[Death] _X > 0 -> (_X' = _X - 1);
-
-endmodule
-
-// Species Source
-module Source
-
-  Source  :  int init 0;
-
-		// Immigration
-		[Immigration] Source > 0 -> (Source' = Source - 1);
-
-endmodule
-
-// Species Sink
-module Sink
-
-  Sink  :  int init 0;
-
-		// Death
-		[Death] Sink > 0 -> (Sink' = Sink + 1);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Immigration:  ->  Source -> _X
-		[Immigration] Alpha > 0 -> Alpha : true;
-
-		// Death:  ->  _X -> Sink
-		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
-// Reward 2: Source
-rewards "Source" true : Source; endrewards
-// Reward 3: Sink
-rewards "Sink" true : Sink; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.xml
deleted file mode 100755
index 4136c9f..0000000
--- a/Benchmarks/SBMLstochasticTests/00024/00024-sbml-l3v2.xml
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="ImmigrationDeath05" name="Immigration-Death (002), variant 05" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species id="Source" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
-      <species id="Sink" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="Alpha" value="10" constant="true"/>
-      <parameter id="Mu" value="0.1" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Immigration" reversible="false">
-        <listOfReactants>
-          <speciesReference species="Source" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <ci> Alpha </ci>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Death" reversible="false">
-        <listOfReactants>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="Sink" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> Mu </ci>
-              <ci> X </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.props
deleted file mode 100644
index 0438bbd..0000000
--- a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00025/00025-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X > 99.3262) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.sm
deleted file mode 100644
index 397f904..0000000
--- a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.sm
+++ /dev/null
@@ -1,62 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00025/00025-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-
-// Model parameters
-const double Alpha = 10.0; // 
-const double Mu = 0.1; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
-		// Death
-		[Death] _X > 0 -> (_X' = _X - 1);
-
-endmodule
-
-// Species Source
-module Source
-
-  Source  :  int init 0;
-
-		// Immigration
-		[Immigration] Source > 0 -> (Source' = Source - 1);
-
-endmodule
-
-// Species Sink
-module Sink
-
-  Sink  :  int init 0;
-
-		// Death
-		[Death] Sink > 0 -> (Sink' = Sink + 1);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Immigration:  ->  Source -> _X
-		[Immigration] Alpha > 0 -> Alpha : true;
-
-		// Death:  ->  _X -> Sink
-		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
-// Reward 2: Source
-rewards "Source" true : Source; endrewards
-// Reward 3: Sink
-rewards "Sink" true : Sink; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.xml
deleted file mode 100755
index d0460f6..0000000
--- a/Benchmarks/SBMLstochasticTests/00025/00025-sbml-l3v2.xml
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="ImmigrationDeath06" name="Immigration-Death (002), variant 06" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species id="Source" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
-      <species id="Sink" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="Alpha" value="10" constant="true"/>
-      <parameter id="Mu" value="0.1" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Immigration" reversible="false">
-        <listOfReactants>
-          <speciesReference species="Source" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <ci> Alpha </ci>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Death" reversible="false">
-        <listOfReactants>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="Sink" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> Mu </ci>
-              <ci> X </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.props
deleted file mode 100644
index 82473ca..0000000
--- a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00026/00026-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X > 99.3262) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.sm
deleted file mode 100644
index 8d09353..0000000
--- a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.sm
+++ /dev/null
@@ -1,62 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00026/00026-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-
-// Model parameters
-const double Alpha = 10.0; // 
-const double Mu = 0.1; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
-		// Death
-		[Death] _X > 0 -> (_X' = _X - 1);
-
-endmodule
-
-// Species Source
-module Source
-
-  Source  :  int init 0;
-
-		// Immigration
-		[Immigration] Source > 0 -> (Source' = Source - 1);
-
-endmodule
-
-// Species Sink
-module Sink
-
-  Sink  :  int init 0;
-
-		// Death
-		[Death] Sink > 0 -> (Sink' = Sink + 1);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Immigration:  ->  Source -> _X
-		[Immigration] Alpha > 0 -> Alpha : true;
-
-		// Death:  ->  _X -> Sink
-		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
-// Reward 2: Source
-rewards "Source" true : Source; endrewards
-// Reward 3: Sink
-rewards "Sink" true : Sink; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.xml
deleted file mode 100755
index 22e15cb..0000000
--- a/Benchmarks/SBMLstochasticTests/00026/00026-sbml-l3v2.xml
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="ImmigrationDeath07" name="Immigration-Death (002), variant 07" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species id="Source" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
-      <species id="Sink" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="true"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="Alpha" value="10" constant="true"/>
-      <parameter id="Mu" value="0.1" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Immigration" reversible="false">
-        <listOfReactants>
-          <speciesReference species="Source" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <ci> Alpha </ci>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Death" reversible="false">
-        <listOfReactants>
-          <speciesReference species="X" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="Sink" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> Mu </ci>
-              <ci> X </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props
index 23d31a7..bd8202f 100644
--- a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00027/00027-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 9.93262) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X > 9.93262) ]
diff --git a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm
index cac6195..21da14d 100644
--- a/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00027/00027-sbml-l3v2.sm
@@ -7,11 +7,11 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double k = 2.0; // 
+const double k = 2.0; //
 
 // Model local parameters
-const double local_k_0 = 1.0; // 
-const double local_k_1 = 0.1; // 
+const double local_k_0 = 1.0; //
+const double local_k_1 = 0.1; //
 
 // Species _X
 module _X
@@ -19,7 +19,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
+		[Immigration] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -31,7 +31,7 @@ module reaction_rates
 		// Immigration:  ->   -> _X
 		[Immigration] local_k_0 > 0 -> local_k_0 : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (local_k_1 * _X) > 0 -> (local_k_1 * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00027/results.txt b/Benchmarks/SBMLstochasticTests/00027/results.txt
new file mode 100644
index 0000000..b30237d
--- /dev/null
+++ b/Benchmarks/SBMLstochasticTests/00027/results.txt
@@ -0,0 +1,2 @@
+0.981591707975164
+0.981591707975164
diff --git a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props
index 6cd5888..19c8a50 100644
--- a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00028/00028-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 13.283399945) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 13.283399945) ]
diff --git a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm
index f9298d3..f940ba8 100644
--- a/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00028/00028-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 1.0; // 
-const double Mu = 0.1; // 
+const double Alpha = 1.0; //
+const double Mu = 0.1; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
+		[Immigration] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Immigration:  ->   -> _X
 		[Immigration] Alpha > 0 -> Alpha : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props
index b4089ff..eed452c 100644
--- a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00029/00029-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X < 10.6392786121) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X < 10.6392786121) ]
diff --git a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm
index aaad123..fd9926e 100644
--- a/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00029/00029-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 1.0; // 
-const double Mu = 0.1; // 
+const double Alpha = 1.0; //
+const double Mu = 0.1; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 1);
+		[Immigration] _X >= 0 -> (_X' = _X + 1);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Immigration:  ->   -> _X
 		[Immigration] Alpha > 0 -> Alpha : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.props
deleted file mode 100644
index a163091..0000000
--- a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00030/00030-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X < 28.542298) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.sm
deleted file mode 100644
index b5321f9..0000000
--- a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.sm
+++ /dev/null
@@ -1,52 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00030/00030-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-
-// Model parameters
-const double k1 = 0.001; // 
-const double k2 = 0.01; // 
-
-// Species _P
-module _P
-
-  _P  :  int init 100;
-
-		// Dimerisation
-		[Dimerisation] _P > 0 -> (_P' = _P - 2);
-		// Disassociation
-		[Disassociation] _P > 0 -> (_P' = _P + 2);
-
-endmodule
-
-// Species P2
-module P2
-
-  P2  :  int init 0;
-
-		// Dimerisation
-		[Dimerisation] P2 > 0 -> (P2' = P2 + 1);
-		// Disassociation
-		[Disassociation] P2 > 0 -> (P2' = P2 - 1);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Dimerisation:  ->  _P -> P2
-		[Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true;
-
-		// Disassociation:  ->  P2 -> _P
-		[Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _P
-rewards "_P" true : _P; endrewards
-// Reward 2: P2
-rewards "P2" true : P2; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.xml
deleted file mode 100755
index 52c5718..0000000
--- a/Benchmarks/SBMLstochasticTests/00030/00030-sbml-l3v2.xml
+++ /dev/null
@@ -1,61 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="Dimerisation01" name="Dimerisation model (003), variant 01" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="P" compartment="Cell" initialAmount="100" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species id="P2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="k1" value="0.001" constant="true"/>
-      <parameter id="k2" value="0.01" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Dimerisation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> k1 </ci>
-                <ci> P </ci>
-                <apply>
-                  <minus/>
-                  <ci> P </ci>
-                  <cn type="integer"> 1 </cn>
-                </apply>
-              </apply>
-              <cn type="integer"> 2 </cn>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Disassociation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> k2 </ci>
-              <ci> P2 </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.props
deleted file mode 100644
index 8820a70..0000000
--- a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00031/00031-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X < 144.995965) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.sm
deleted file mode 100644
index 79534c0..0000000
--- a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.sm
+++ /dev/null
@@ -1,52 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00031/00031-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-
-// Model parameters
-const double k1 = 2.0E-4; // 
-const double k2 = 0.004; // 
-
-// Species _P
-module _P
-
-  _P  :  int init 1000;
-
-		// Dimerisation
-		[Dimerisation] _P > 0 -> (_P' = _P - 2);
-		// Disassociation
-		[Disassociation] _P > 0 -> (_P' = _P + 2);
-
-endmodule
-
-// Species P2
-module P2
-
-  P2  :  int init 0;
-
-		// Dimerisation
-		[Dimerisation] P2 > 0 -> (P2' = P2 + 1);
-		// Disassociation
-		[Disassociation] P2 > 0 -> (P2' = P2 - 1);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Dimerisation:  ->  _P -> P2
-		[Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true;
-
-		// Disassociation:  ->  P2 -> _P
-		[Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _P
-rewards "_P" true : _P; endrewards
-// Reward 2: P2
-rewards "P2" true : P2; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.xml
deleted file mode 100755
index 1b978f8..0000000
--- a/Benchmarks/SBMLstochasticTests/00031/00031-sbml-l3v2.xml
+++ /dev/null
@@ -1,61 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="Dimerisation02" name="Dimerisation model (003), variant 02" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="P" compartment="Cell" initialAmount="1000" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species id="P2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="k1" value="0.0002" constant="true"/>
-      <parameter id="k2" value="0.004" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Dimerisation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> k1 </ci>
-                <ci> P </ci>
-                <apply>
-                  <minus/>
-                  <ci> P </ci>
-                  <cn type="integer"> 1 </cn>
-                </apply>
-              </apply>
-              <cn type="integer"> 2 </cn>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Disassociation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> k2 </ci>
-              <ci> P2 </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.props
deleted file mode 100644
index 4d8bd18..0000000
--- a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00032/00032-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X < 34.887453) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.sm
deleted file mode 100644
index 5351e6e..0000000
--- a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.sm
+++ /dev/null
@@ -1,52 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00032/00032-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-
-// Model parameters
-const double k1 = 0.001; // 
-const double k2 = 0.01; // 
-
-// Species _P
-module _P
-
-  _P  :  int init 100;
-
-		// Dimerisation
-		[Dimerisation] _P > 0 -> (_P' = _P - 2);
-		// Disassociation
-		[Disassociation] _P > 0 -> (_P' = _P + 2);
-
-endmodule
-
-// Species P2
-module P2
-
-  P2  :  int init 0;
-
-		// Dimerisation
-		[Dimerisation] P2 > 0 -> (P2' = P2 + 1);
-		// Disassociation
-		[Disassociation] P2 > 0 -> (P2' = P2 - 1);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Dimerisation:  ->  _P -> P2
-		[Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true;
-
-		// Disassociation:  ->  P2 -> _P
-		[Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _P
-rewards "_P" true : _P; endrewards
-// Reward 2: P2
-rewards "P2" true : P2; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.xml
deleted file mode 100755
index 7ba81c8..0000000
--- a/Benchmarks/SBMLstochasticTests/00032/00032-sbml-l3v2.xml
+++ /dev/null
@@ -1,86 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="Dimerisation03" name="Dimerisation model (003), variant 03" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="P" compartment="Cell" initialAmount="100" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species id="P2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="k1" value="0.001" constant="true"/>
-      <parameter id="k2" value="0.01" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Dimerisation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> k1 </ci>
-                <ci> P </ci>
-                <apply>
-                  <minus/>
-                  <ci> P </ci>
-                  <cn type="integer"> 1 </cn>
-                </apply>
-              </apply>
-              <cn type="integer"> 2 </cn>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Disassociation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> k2 </ci>
-              <ci> P2 </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <listOfEvents>
-      <event id="reset" useValuesFromTriggerTime="true">
-        <trigger initialValue="false" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 25 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="P">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 100 </cn>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="P2">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.props
deleted file mode 100644
index af5c237..0000000
--- a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00033/00033-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X > 58.3027904) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.sm
deleted file mode 100644
index bdb0ba6..0000000
--- a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.sm
+++ /dev/null
@@ -1,52 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00033/00033-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-
-// Model parameters
-const double k1 = 0.001; // 
-const double k2 = 0.01; // 
-
-// Species _P
-module _P
-
-  _P  :  int init 100;
-
-		// Dimerisation
-		[Dimerisation] _P > 0 -> (_P' = _P - 2);
-		// Disassociation
-		[Disassociation] _P > 0 -> (_P' = _P + 2);
-
-endmodule
-
-// Species P2
-module P2
-
-  P2  :  int init 0;
-
-		// Dimerisation
-		[Dimerisation] P2 > 0 -> (P2' = P2 + 1);
-		// Disassociation
-		[Disassociation] P2 > 0 -> (P2' = P2 - 1);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Dimerisation:  ->  _P -> P2
-		[Dimerisation] ((k1 * _P* ( _P- 1)) / 2) > 0 -> ((k1 * _P* ( _P- 1)) / 2) : true;
-
-		// Disassociation:  ->  P2 -> _P
-		[Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _P
-rewards "_P" true : _P; endrewards
-// Reward 2: P2
-rewards "P2" true : P2; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.xml
deleted file mode 100755
index 5023e4a..0000000
--- a/Benchmarks/SBMLstochasticTests/00033/00033-sbml-l3v2.xml
+++ /dev/null
@@ -1,86 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
-  <model id="Dimerisation04" name="Dimerisation model (003), variant 04" substanceUnits="item" timeUnits="second" volumeUnits="litre">
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="P" compartment="Cell" initialAmount="100" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species id="P2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="k1" value="0.001" constant="true"/>
-      <parameter id="k2" value="0.01" constant="true"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Dimerisation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> k1 </ci>
-                <ci> P </ci>
-                <apply>
-                  <minus/>
-                  <ci> P </ci>
-                  <cn type="integer"> 1 </cn>
-                </apply>
-              </apply>
-              <cn type="integer"> 2 </cn>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction id="Disassociation" reversible="false">
-        <listOfReactants>
-          <speciesReference species="P2" stoichiometry="1" constant="false"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="P" stoichiometry="2" constant="false"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> k2 </ci>
-              <ci> P2 </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <listOfEvents>
-      <event id="reset" useValuesFromTriggerTime="true">
-        <trigger initialValue="false" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <gt/>
-              <ci> P2 </ci>
-              <cn type="integer"> 30 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="P">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 100 </cn>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="P2">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props
index d7afcd6..1ef42d0 100644
--- a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00034/00034-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 35.728851) ]
\ No newline at end of file
+P=? [ true U [0,50] (P2 >= 40) ]
diff --git a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm
index 265a82b..b37f2bc 100644
--- a/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00034/00034-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double k1 = 0.001; // 
-const double k2 = 0.01; // 
+const double k1 = 0.001; //
+const double k2 = 0.01; //
 
 // Species P2
 module P2
@@ -16,7 +16,7 @@ module P2
   P2  :  int init 0;
 
 		// Dimerisation
-		[Dimerisation] P2 > 0 -> (P2' = P2 + 1);
+		[Dimerisation] P2 >= 0 -> (P2' = P2 + 1);
 		// Disassociation
 		[Disassociation] P2 > 0 -> (P2' = P2 - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Dimerisation:  ->   -> P2
 		[Dimerisation] (0.5 * k1 * (100 - (2 * P2)) * (99 - (2 * P2))) > 0 -> (0.5 * k1 * (100 - (2 * P2)) * (99 - (2 * P2))) : true;
 
-		// Disassociation:  ->  P2 -> 
+		// Disassociation:  ->  P2 ->
 		[Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props
index 065c787..f37ff17 100644
--- a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00035/00035-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 35.728851) ]
\ No newline at end of file
+P=? [ true U [0,50] (P2 >= 36) ]
diff --git a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm
index 85e9280..5952074 100644
--- a/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00035/00035-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double k1 = 0.001; // 
-const double k2 = 0.01; // 
+const double k1 = 0.001; //
+const double k2 = 0.01; //
 
 // Species P2
 module P2
@@ -16,7 +16,7 @@ module P2
   P2  :  int init 0;
 
 		// Dimerisation
-		[Dimerisation] P2 > 0 -> (P2' = P2 + 1);
+		[Dimerisation] P2 >= 0 -> (P2' = P2 + 1);
 		// Disassociation
 		[Disassociation] P2 > 0 -> (P2' = P2 - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Dimerisation:  ->   -> P2
 		[Dimerisation] ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) > 0 -> ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) : true;
 
-		// Disassociation:  ->  P2 -> 
+		// Disassociation:  ->  P2 ->
 		[Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props
index bce2685..620fbdd 100644
--- a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00036/00036-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 35.728851) ]
\ No newline at end of file
+P=? [ true U [0,50] (P2 >= 40) ]
diff --git a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm
index 614a45c..5661ea1 100644
--- a/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00036/00036-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double k1 = 0.001; // 
-const double k2 = 0.01; // 
+const double k1 = 0.001; //
+const double k2 = 0.01; //
 
 // Species P2
 module P2
@@ -16,7 +16,7 @@ module P2
   P2  :  int init 0;
 
 		// Dimerisation
-		[Dimerisation] P2 > 0 -> (P2' = P2 + 1);
+		[Dimerisation] P2 >= 0 -> (P2' = P2 + 1);
 		// Disassociation
 		[Disassociation] P2 > 0 -> (P2' = P2 - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Dimerisation:  ->   -> P2
 		[Dimerisation] ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) > 0 -> ((k1 * (100 - (2 * P2)) * ((100 - (2 * P2)) - 1)) / 2) : true;
 
-		// Disassociation:  ->  P2 -> 
+		// Disassociation:  ->  P2 ->
 		[Disassociation] (k2 * P2) > 0 -> (k2 * P2) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props
index d9f2e98..c98c111 100644
--- a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00037/00037-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X > 24.998865) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X >= 40) ]
diff --git a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm
index 99aa25b..416d262 100644
--- a/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00037/00037-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 1.0; // 
-const double Mu = 0.2; // 
+const double Alpha = 1.0; //
+const double Mu = 0.2; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 5);
+		[Immigration] _X >= 0 -> (_X' = _X + 5);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Immigration:  ->   -> _X
 		[Immigration] Alpha > 0 -> Alpha : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props
index 01e79da..3ee1426 100644
--- a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00038/00038-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X = 25.0) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X >= 55) ]
diff --git a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm
index d2c93c9..a7b2375 100644
--- a/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00038/00038-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 1.0; // 
-const double Mu = 0.4; // 
+const double Alpha = 1.0; //
+const double Mu = 0.4; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 10);
+		[Immigration] _X >= 0 -> (_X' = _X + 10);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -25,11 +25,10 @@ endmodule
 // Reaction rates
 module reaction_rates
 
-		// Immigration:  ->   -> 
-_X
+		// Immigration:  ->
 		[Immigration] Alpha > 0 -> Alpha : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props
index ad714ad..c882c75 100644
--- a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props
+++ b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.props
@@ -2,4 +2,4 @@
 // Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00039/00039-sbml-l3v2.xml
 // @GeneticLogicLab
 
-P=? [ true U [0,50] (X = 25.0) ]
\ No newline at end of file
+P=? [ true U [0,50] (_X >= 300) ]
diff --git a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm
index 0a17d78..92ba27f 100644
--- a/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm
+++ b/Benchmarks/SBMLstochasticTests/00039/00039-sbml-l3v2.sm
@@ -7,8 +7,8 @@ ctmc
 // Compartment size
 
 // Model parameters
-const double Alpha = 1.0; // 
-const double Mu = 4.0; // 
+const double Alpha = 1.0; //
+const double Mu = 4.0; //
 
 // Species _X
 module _X
@@ -16,7 +16,7 @@ module _X
   _X  :  int init 0;
 
 		// Immigration
-		[Immigration] _X > 0 -> (_X' = _X + 100);
+		[Immigration] _X >= 0 -> (_X' = _X + 100);
 		// Death
 		[Death] _X > 0 -> (_X' = _X - 1);
 
@@ -28,7 +28,7 @@ module reaction_rates
 		// Immigration:  ->   -> d_X
 		[Immigration] Alpha > 0 -> Alpha : true;
 
-		// Death:  ->  _X -> 
+		// Death:  ->  _X ->
 		[Death] (Mu * _X) > 0 -> (Mu * _X) : true;
 
 endmodule
diff --git a/Benchmarks/SBMLstochasticTests/00039/results.txt b/Benchmarks/SBMLstochasticTests/00039/results.txt
new file mode 100644
index 0000000..7aeb020
--- /dev/null
+++ b/Benchmarks/SBMLstochasticTests/00039/results.txt
@@ -0,0 +1,2 @@
+0.06627554753035092
+0.06627554753035092
diff --git a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.props
deleted file mode 100644
index e21e7d4..0000000
--- a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00040/00040-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.sm
deleted file mode 100644
index 4ca7a81..0000000
--- a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00040/00040-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.xml
deleted file mode 100644
index 026fe07..0000000
--- a/Benchmarks/SBMLstochasticTests/00040/00040-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 1.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.props
deleted file mode 100644
index e096445..0000000
--- a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00041/00041-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.sm
deleted file mode 100644
index 532d383..0000000
--- a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00041/00041-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double variance = 1.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.xml
deleted file mode 100644
index 34c9a19..0000000
--- a/Benchmarks/SBMLstochasticTests/00041/00041-sbml-l3v2.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="variance" value="1.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <apply>
-                  <root/>
-                  <degree>
-                    <cn type="integer"> 2 </cn>
-                  </degree>
-                  <ci> variance </ci>
-                </apply>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.props
deleted file mode 100644
index 3f78773..0000000
--- a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00042/00042-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.5) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.sm
deleted file mode 100644
index 179e9e9..0000000
--- a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00042/00042-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.xml
deleted file mode 100644
index 1d1bb7a..0000000
--- a/Benchmarks/SBMLstochasticTests/00042/00042-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/uniform"> uniform </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn type="integer"> 1 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.props
deleted file mode 100644
index 0ced6ac..0000000
--- a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00043/00043-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.sm
deleted file mode 100644
index 8d5c97c..0000000
--- a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00043/00043-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.xml
deleted file mode 100644
index 5d9437b..0000000
--- a/Benchmarks/SBMLstochasticTests/00043/00043-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <cn type="integer"> 1 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.props
deleted file mode 100644
index e9c3b4e..0000000
--- a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00044/00044-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.sm
deleted file mode 100644
index 52148c4..0000000
--- a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00044/00044-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.xml
deleted file mode 100644
index 9f69cea..0000000
--- a/Benchmarks/SBMLstochasticTests/00044/00044-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.props
deleted file mode 100644
index 616d684..0000000
--- a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00045/00045-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.sm
deleted file mode 100644
index f253547..0000000
--- a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00045/00045-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.xml
deleted file mode 100644
index e36080a..0000000
--- a/Benchmarks/SBMLstochasticTests/00045/00045-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/gamma"> gamma </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.props
deleted file mode 100644
index f777707..0000000
--- a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00046/00046-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2.2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.sm
deleted file mode 100644
index e0fef91..0000000
--- a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00046/00046-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.xml
deleted file mode 100644
index fa70c12..0000000
--- a/Benchmarks/SBMLstochasticTests/00046/00046-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/gamma"> gamma </csymbol>
-                <cn type="integer"> 2 </cn>
-                <cn> 1.1 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.props
deleted file mode 100644
index 6f36b72..0000000
--- a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00047/00047-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1.5) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.sm
deleted file mode 100644
index 4380dce..0000000
--- a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00047/00047-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.xml
deleted file mode 100644
index be3990e..0000000
--- a/Benchmarks/SBMLstochasticTests/00047/00047-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/poisson"> poisson </csymbol>
-                <cn> 1.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.props
deleted file mode 100644
index 9312370..0000000
--- a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00048/00048-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.sm
deleted file mode 100644
index 9bfcb9c..0000000
--- a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00048/00048-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.xml
deleted file mode 100644
index bd0828a..0000000
--- a/Benchmarks/SBMLstochasticTests/00048/00048-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/cauchy"> cauchy </csymbol>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.props
deleted file mode 100644
index e92c4f5..0000000
--- a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00049/00049-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.sm
deleted file mode 100644
index 14fceb2..0000000
--- a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00049/00049-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.xml
deleted file mode 100644
index 501f694..0000000
--- a/Benchmarks/SBMLstochasticTests/00049/00049-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/cauchy"> cauchy </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.props
deleted file mode 100644
index 7a9b1b0..0000000
--- a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00050/00050-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.sm
deleted file mode 100644
index 071d6a3..0000000
--- a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00050/00050-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.xml
deleted file mode 100644
index 9297b03..0000000
--- a/Benchmarks/SBMLstochasticTests/00050/00050-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/chisquare"> chisquare </csymbol>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.props
deleted file mode 100644
index 8375089..0000000
--- a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00051/00051-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 3.2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.sm
deleted file mode 100644
index 573dda1..0000000
--- a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00051/00051-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.xml
deleted file mode 100644
index 30bdbcc..0000000
--- a/Benchmarks/SBMLstochasticTests/00051/00051-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/chisquare"> chisquare </csymbol>
-                <cn> 3.2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.props
deleted file mode 100644
index 6804b95..0000000
--- a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00052/00052-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2.506628275) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.sm
deleted file mode 100644
index 02c6c2c..0000000
--- a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00052/00052-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.xml
deleted file mode 100644
index a28e544..0000000
--- a/Benchmarks/SBMLstochasticTests/00052/00052-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/rayleigh"> rayleigh </csymbol>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.props
deleted file mode 100644
index adbd938..0000000
--- a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00053/00053-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.23) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.sm
deleted file mode 100644
index c9b3944..0000000
--- a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00053/00053-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.xml
deleted file mode 100644
index 5910523..0000000
--- a/Benchmarks/SBMLstochasticTests/00053/00053-sbml-l3v2.xml
+++ /dev/null
@@ -1,50 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/bernoulli"> bernoulli </csymbol>
-                <cn> 0.23 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.props
deleted file mode 100644
index dd51a91..0000000
--- a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00054/00054-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.sm
deleted file mode 100644
index 39230c8..0000000
--- a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00054/00054-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.xml
deleted file mode 100644
index a9bb9bf..0000000
--- a/Benchmarks/SBMLstochasticTests/00054/00054-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/laplace"> laplace </csymbol>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.props
deleted file mode 100644
index e2204ea..0000000
--- a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00055/00055-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.sm
deleted file mode 100644
index ab51a22..0000000
--- a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00055/00055-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.xml
deleted file mode 100644
index dc5433d..0000000
--- a/Benchmarks/SBMLstochasticTests/00055/00055-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/laplace"> laplace </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.props
deleted file mode 100644
index 99e1b4b..0000000
--- a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00056/00056-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.sm
deleted file mode 100644
index a22c106..0000000
--- a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00056/00056-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.xml
deleted file mode 100644
index 83f067c..0000000
--- a/Benchmarks/SBMLstochasticTests/00056/00056-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/lognormal"> lognormal </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.props
deleted file mode 100644
index a28f39e..0000000
--- a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00057/00057-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 20) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.sm
deleted file mode 100644
index 5b07837..0000000
--- a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00057/00057-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.xml
deleted file mode 100644
index 104fec3..0000000
--- a/Benchmarks/SBMLstochasticTests/00057/00057-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/binomial"> binomial </csymbol>
-                <cn type="integer"> 100 </cn>
-                <cn> 0.2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.props
deleted file mode 100644
index 5de8be8..0000000
--- a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00058/00058-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 20.6064) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.sm
deleted file mode 100644
index a102679..0000000
--- a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00058/00058-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.xml
deleted file mode 100644
index 4ed6b60..0000000
--- a/Benchmarks/SBMLstochasticTests/00058/00058-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/binomial"> binomial </csymbol>
-                <cn type="integer"> 100 </cn>
-                <cn> 0.2 </cn>
-                <cn type="integer"> 15 </cn>
-                <cn type="integer"> 32 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.props
deleted file mode 100644
index 9801bc0..0000000
--- a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00059/00059-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 3.348) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.sm
deleted file mode 100644
index eb9a145..0000000
--- a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00059/00059-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.xml
deleted file mode 100644
index 1babf9f..0000000
--- a/Benchmarks/SBMLstochasticTests/00059/00059-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/cauchy"> cauchy </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn> 1.1 </cn>
-                <cn type="integer"> 10 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.props
deleted file mode 100644
index d001825..0000000
--- a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00060/00060-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 3.6835) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.sm
deleted file mode 100644
index a81eacf..0000000
--- a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00060/00060-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.xml
deleted file mode 100644
index 2ebfb94..0000000
--- a/Benchmarks/SBMLstochasticTests/00060/00060-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/chisquare"> chisquare </csymbol>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 8 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.props
deleted file mode 100644
index 7899f8f..0000000
--- a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00061/00061-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2.995) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.sm
deleted file mode 100644
index 1f56d31..0000000
--- a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00061/00061-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.xml
deleted file mode 100644
index 1080ac2..0000000
--- a/Benchmarks/SBMLstochasticTests/00061/00061-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
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-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 9 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.props
deleted file mode 100644
index 3b9c6bc..0000000
--- a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00062/00062-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 4.1382735) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.sm
deleted file mode 100644
index 67eb058..0000000
--- a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00062/00062-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.xml
deleted file mode 100644
index e32de8b..0000000
--- a/Benchmarks/SBMLstochasticTests/00062/00062-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
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-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/gamma"> gamma </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 3 </cn>
-                <cn type="integer"> 6 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.props
deleted file mode 100644
index fe1b3ec..0000000
--- a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00063/00063-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 3.84976) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.sm
deleted file mode 100644
index 5c99646..0000000
--- a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00063/00063-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.xml
deleted file mode 100644
index eafdec1..0000000
--- a/Benchmarks/SBMLstochasticTests/00063/00063-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/laplace"> laplace </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 10 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.props
deleted file mode 100644
index 122d87f..0000000
--- a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00064/00064-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1.68) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.sm
deleted file mode 100644
index a82e277..0000000
--- a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00064/00064-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.xml
deleted file mode 100644
index f02d2c3..0000000
--- a/Benchmarks/SBMLstochasticTests/00064/00064-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/lognormal"> lognormal </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 3 </cn>
-                <cn type="integer"> 10 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.props
deleted file mode 100644
index d97629b..0000000
--- a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00065/00065-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2.6364) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.sm
deleted file mode 100644
index a00f75e..0000000
--- a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00065/00065-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.xml
deleted file mode 100644
index 6b4a0cf..0000000
--- a/Benchmarks/SBMLstochasticTests/00065/00065-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/poisson"> poisson </csymbol>
-                <cn> 1.5 </cn>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 18 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.props
deleted file mode 100644
index fb1973d..0000000
--- a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00066/00066-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 3.76665) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.sm
deleted file mode 100644
index 02229f2..0000000
--- a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00066/00066-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.xml
deleted file mode 100644
index 0e6631c..0000000
--- a/Benchmarks/SBMLstochasticTests/00066/00066-sbml-l3v2.xml
+++ /dev/null
@@ -1,52 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialConcentration="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/rayleigh"> rayleigh </csymbol>
-                <cn type="integer"> 2 </cn>
-                <cn type="integer"> 3 </cn>
-                <cn type="integer"> 5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.props
deleted file mode 100644
index 04ea464..0000000
--- a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00067/00067-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.sm
deleted file mode 100644
index 7aad191..0000000
--- a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00067/00067-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double truncationLowerBound = -0.5; // 
-const double truncationUpperBound = 0.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.xml
deleted file mode 100644
index 87f7a55..0000000
--- a/Benchmarks/SBMLstochasticTests/00067/00067-sbml-l3v2.xml
+++ /dev/null
@@ -1,57 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="truncationLowerBound" value="-0.5" constant="true"/>
-      <parameter id="truncationUpperBound" value="0.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 0.5 </cn>
-                <ci> truncationLowerBound </ci>
-                <ci> truncationUpperBound </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.props
deleted file mode 100644
index f26aeb4..0000000
--- a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00068/00068-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.479252959) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.sm
deleted file mode 100644
index 7b274af..0000000
--- a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.sm
+++ /dev/null
@@ -1,31 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00068/00068-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double _rate = 1.0; // 
-const double truncationLowerBound = 0.25; // 
-const double truncationUpperBound = 0.75; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.xml
deleted file mode 100644
index 5459788..0000000
--- a/Benchmarks/SBMLstochasticTests/00068/00068-sbml-l3v2.xml
+++ /dev/null
@@ -1,57 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="rate" value="1" constant="true"/>
-      <parameter id="truncationLowerBound" value="0.25" constant="true"/>
-      <parameter id="truncationUpperBound" value="0.75" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <ci> rate </ci>
-                <ci> truncationLowerBound </ci>
-                <ci> truncationUpperBound </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.props
deleted file mode 100644
index 008437f..0000000
--- a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00069/00069-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.897735417) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.sm
deleted file mode 100644
index 487f36b..0000000
--- a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00069/00069-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.xml
deleted file mode 100644
index 22a5f84..0000000
--- a/Benchmarks/SBMLstochasticTests/00069/00069-sbml-l3v2.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 1.5 </cn>
-                <apply>
-                  <minus/>
-                  <cn> 0.5 </cn>
-                </apply>
-                <infinity/>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.props
deleted file mode 100644
index a3566dd..0000000
--- a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00070/00070-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = -0.897735417) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.sm
deleted file mode 100644
index 70f217e..0000000
--- a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00070/00070-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.xml
deleted file mode 100644
index 907743a..0000000
--- a/Benchmarks/SBMLstochasticTests/00070/00070-sbml-l3v2.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 1.5 </cn>
-                <apply>
-                  <minus/>
-                  <infinity/>
-                </apply>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.props
deleted file mode 100644
index efca5c1..0000000
--- a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00071/00071-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1.532245529) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.sm
deleted file mode 100644
index e170656..0000000
--- a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00071/00071-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.xml
deleted file mode 100644
index b64942f..0000000
--- a/Benchmarks/SBMLstochasticTests/00071/00071-sbml-l3v2.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 1.5 </cn>
-                <cn> 0.5 </cn>
-                <infinity/>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.props
deleted file mode 100644
index 24903bf..0000000
--- a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00072/00072-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = -1.532245529) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.sm
deleted file mode 100644
index 45e410f..0000000
--- a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00072/00072-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.xml
deleted file mode 100644
index 8997450..0000000
--- a/Benchmarks/SBMLstochasticTests/00072/00072-sbml-l3v2.xml
+++ /dev/null
@@ -1,61 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 1.5 </cn>
-                <apply>
-                  <minus/>
-                  <infinity/>
-                </apply>
-                <apply>
-                  <minus/>
-                  <cn> 0.5 </cn>
-                </apply>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.props
deleted file mode 100644
index cb499bb..0000000
--- a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00073/00073-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.sm
deleted file mode 100644
index 26fda6a..0000000
--- a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00073/00073-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.xml
deleted file mode 100644
index ac20bb1..0000000
--- a/Benchmarks/SBMLstochasticTests/00073/00073-sbml-l3v2.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 0.5 </cn>
-                <apply>
-                  <minus/>
-                  <cn> 0.5 </cn>
-                </apply>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.props
deleted file mode 100644
index d23c452..0000000
--- a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00074/00074-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.sm
deleted file mode 100644
index 0517600..0000000
--- a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00074/00074-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double variance = 0.25; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.xml
deleted file mode 100644
index e1f5315..0000000
--- a/Benchmarks/SBMLstochasticTests/00074/00074-sbml-l3v2.xml
+++ /dev/null
@@ -1,60 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="variance" value="0.25" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <apply>
-                  <root/>
-                  <degree>
-                    <cn type="integer"> 2 </cn>
-                  </degree>
-                  <ci> variance </ci>
-                </apply>
-                <cn> -0.5 </cn>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.props
deleted file mode 100644
index f948974..0000000
--- a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00075/00075-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.178136442) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.sm
deleted file mode 100644
index b039087..0000000
--- a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00075/00075-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.xml
deleted file mode 100644
index 933bdc6..0000000
--- a/Benchmarks/SBMLstochasticTests/00075/00075-sbml-l3v2.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 0.5 </cn>
-                <apply>
-                  <minus/>
-                  <cn> 0.25 </cn>
-                </apply>
-                <cn> 0.75 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.props
deleted file mode 100644
index 9d0cf68..0000000
--- a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00076/00076-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.460322303) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.sm
deleted file mode 100644
index 6ae2ef5..0000000
--- a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00076/00076-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.xml
deleted file mode 100644
index 838b01c..0000000
--- a/Benchmarks/SBMLstochasticTests/00076/00076-sbml-l3v2.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 0.5 </cn>
-                <cn> 0.25 </cn>
-                <cn> 0.75 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.props
deleted file mode 100644
index 7386756..0000000
--- a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00077/00077-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1.25) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.sm
deleted file mode 100644
index c3b0e9b..0000000
--- a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00077/00077-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.xml
deleted file mode 100644
index 0037b24..0000000
--- a/Benchmarks/SBMLstochasticTests/00077/00077-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn> 0.25 </cn>
-                <infinity/>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.props
deleted file mode 100644
index 6c2b095..0000000
--- a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00078/00078-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.328558649) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.sm
deleted file mode 100644
index 8b7dfb6..0000000
--- a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00078/00078-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.xml
deleted file mode 100644
index 47129d1..0000000
--- a/Benchmarks/SBMLstochasticTests/00078/00078-sbml-l3v2.xml
+++ /dev/null
@@ -1,57 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <minus/>
-                  <infinity/>
-                </apply>
-                <cn> 0.75 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.props
deleted file mode 100644
index 53c6b7c..0000000
--- a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00079/00079-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.479252959) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.sm
deleted file mode 100644
index af5c36e..0000000
--- a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.sm
+++ /dev/null
@@ -1,28 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00079/00079-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.xml
deleted file mode 100644
index ca86743..0000000
--- a/Benchmarks/SBMLstochasticTests/00079/00079-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <cn type="integer"> 1 </cn>
-                <cn> 0.25 </cn>
-                <cn> 0.75 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.props
deleted file mode 100644
index 2d5515d..0000000
--- a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00080/00080-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.sm
deleted file mode 100644
index c901357..0000000
--- a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00080/00080-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double mean = 0.0; // 
-const double stddev = 1.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.xml
deleted file mode 100644
index 54d06fe..0000000
--- a/Benchmarks/SBMLstochasticTests/00080/00080-sbml-l3v2.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="mean" value="0" constant="true"/>
-      <parameter id="stddev" value="1.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <ci> mean </ci>
-                <ci> stddev </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.props
deleted file mode 100644
index b03ae9c..0000000
--- a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00081/00081-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.sm
deleted file mode 100644
index 65e87f0..0000000
--- a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00081/00081-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double mean = 0.0; // 
-const double variance = 1.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.xml
deleted file mode 100644
index 5d644e8..0000000
--- a/Benchmarks/SBMLstochasticTests/00081/00081-sbml-l3v2.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="mean" value="0" constant="true"/>
-      <parameter id="variance" value="1.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <ci> mean </ci>
-                <apply>
-                  <root/>
-                  <degree>
-                    <cn type="integer"> 2 </cn>
-                  </degree>
-                  <ci> variance </ci>
-                </apply>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.props
deleted file mode 100644
index 4823e46..0000000
--- a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00082/00082-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.5) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.sm
deleted file mode 100644
index f6e1f1c..0000000
--- a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00082/00082-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double minimum = 0.0; // 
-const double maximum = 1.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.xml
deleted file mode 100644
index ec40ea6..0000000
--- a/Benchmarks/SBMLstochasticTests/00082/00082-sbml-l3v2.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="minimum" value="0" constant="true"/>
-      <parameter id="maximum" value="1" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/uniform"> uniform </csymbol>
-                <ci> minimum </ci>
-                <ci> maximum </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.props
deleted file mode 100644
index fb825da..0000000
--- a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00083/00083-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.sm
deleted file mode 100644
index c079978..0000000
--- a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00083/00083-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double _rate = 1.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.xml
deleted file mode 100644
index 26a03c8..0000000
--- a/Benchmarks/SBMLstochasticTests/00083/00083-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="rate" value="1" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <ci> rate </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.props
deleted file mode 100644
index 506c085..0000000
--- a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00084/00084-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.sm
deleted file mode 100644
index e257817..0000000
--- a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00084/00084-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double _rate = 0.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.xml
deleted file mode 100644
index 327d60f..0000000
--- a/Benchmarks/SBMLstochasticTests/00084/00084-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="rate" value="0.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <ci> rate </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.props
deleted file mode 100644
index 1985b09..0000000
--- a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00085/00085-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.sm
deleted file mode 100644
index 934faab..0000000
--- a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00085/00085-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double shape = 1.0; // 
-const double scale = 2.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.xml
deleted file mode 100644
index 6477daf..0000000
--- a/Benchmarks/SBMLstochasticTests/00085/00085-sbml-l3v2.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="shape" value="1" constant="true"/>
-      <parameter id="scale" value="2" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/gamma"> gamma </csymbol>
-                <ci> shape </ci>
-                <ci> scale </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.props
deleted file mode 100644
index b72ab8a..0000000
--- a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00086/00086-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2.2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.sm
deleted file mode 100644
index 2685c99..0000000
--- a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00086/00086-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double shape = 2.0; // 
-const double scale = 1.1; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.xml
deleted file mode 100644
index 0994a92..0000000
--- a/Benchmarks/SBMLstochasticTests/00086/00086-sbml-l3v2.xml
+++ /dev/null
@@ -1,55 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="shape" value="2" constant="true"/>
-      <parameter id="scale" value="1.1" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/gamma"> gamma </csymbol>
-                <ci> shape </ci>
-                <ci> scale </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.props
deleted file mode 100644
index 22dd2d6..0000000
--- a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00087/00087-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 1.5) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.sm
deleted file mode 100644
index df9efa7..0000000
--- a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00087/00087-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double _rate = 1.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.xml
deleted file mode 100644
index a1a5ff7..0000000
--- a/Benchmarks/SBMLstochasticTests/00087/00087-sbml-l3v2.xml
+++ /dev/null
@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="rate" value="1.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/poisson"> poisson </csymbol>
-                <ci> rate </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.props
deleted file mode 100644
index d19787e..0000000
--- a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00088/00088-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.sm
deleted file mode 100644
index 2961bf2..0000000
--- a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00088/00088-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double stddev = 1.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.xml
deleted file mode 100644
index d9b6a87..0000000
--- a/Benchmarks/SBMLstochasticTests/00088/00088-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="stddev" value="1.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <ci> stddev </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.props
deleted file mode 100644
index 6a0e7cd..0000000
--- a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00089/00089-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.479252959) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.sm
deleted file mode 100644
index abba6d1..0000000
--- a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00089/00089-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double truncationLowerBound = 0.25; // 
-const double truncationUpperBound = 0.75; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.xml
deleted file mode 100644
index 323c126..0000000
--- a/Benchmarks/SBMLstochasticTests/00089/00089-sbml-l3v2.xml
+++ /dev/null
@@ -1,56 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="truncationLowerBound" value="0.25" constant="true"/>
-      <parameter id="truncationUpperBound" value="0.75" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/exponential"> exponential </csymbol>
-                <cn type="integer"> 1 </cn>
-                <ci> truncationLowerBound </ci>
-                <ci> truncationUpperBound </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.props
deleted file mode 100644
index b13b64c..0000000
--- a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00090/00090-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.sm
deleted file mode 100644
index f47820c..0000000
--- a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00090/00090-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double mean = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.xml
deleted file mode 100644
index 535f642..0000000
--- a/Benchmarks/SBMLstochasticTests/00090/00090-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="mean" value="0" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <ci> mean </ci>
-                <cn> 1.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.props
deleted file mode 100644
index 9dd4e33..0000000
--- a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00091/00091-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.sm
deleted file mode 100644
index ebad134..0000000
--- a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00091/00091-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double mean = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.xml
deleted file mode 100644
index a9739cf..0000000
--- a/Benchmarks/SBMLstochasticTests/00091/00091-sbml-l3v2.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.12.0 with libSBML version 5.18.1. -->
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model metaid="doc0" id="doc0">
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="mean" value="0" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <ci> mean </ci>
-                <apply>
-                  <root/>
-                  <degree>
-                    <cn type="integer"> 2 </cn>
-                  </degree>
-                  <cn> 1.5 </cn>
-                </apply>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn> -0.5 </cn>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.props
deleted file mode 100644
index ac1160a..0000000
--- a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00092/00092-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.5) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.sm
deleted file mode 100644
index d0f93a1..0000000
--- a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00092/00092-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double maximum = 1.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.xml
deleted file mode 100644
index b0e6c16..0000000
--- a/Benchmarks/SBMLstochasticTests/00092/00092-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="maximum" value="1" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/uniform"> uniform </csymbol>
-                <cn type="integer"> 0 </cn>
-                <ci> maximum </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.props
deleted file mode 100644
index 79da70a..0000000
--- a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00093/00093-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0.5) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.sm
deleted file mode 100644
index b9212d7..0000000
--- a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00093/00093-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double minimum = 0.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.xml
deleted file mode 100644
index 70b0ec1..0000000
--- a/Benchmarks/SBMLstochasticTests/00093/00093-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="minimum" value="0" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/uniform"> uniform </csymbol>
-                <ci> minimum </ci>
-                <cn type="integer"> 1 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.props
deleted file mode 100644
index 045183f..0000000
--- a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00094/00094-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.sm
deleted file mode 100644
index a9d1fec..0000000
--- a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00094/00094-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double scale = 2.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.xml
deleted file mode 100644
index 08d0c47..0000000
--- a/Benchmarks/SBMLstochasticTests/00094/00094-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="scale" value="2" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/gamma"> gamma </csymbol>
-                <cn type="integer"> 1 </cn>
-                <ci> scale </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.props
deleted file mode 100644
index 67cca9e..0000000
--- a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00095/00095-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 2) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.sm
deleted file mode 100644
index 1007735..0000000
--- a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.sm
+++ /dev/null
@@ -1,29 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00095/00095-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double shape = 1.0; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.xml
deleted file mode 100644
index 1faa4f9..0000000
--- a/Benchmarks/SBMLstochasticTests/00095/00095-sbml-l3v2.xml
+++ /dev/null
@@ -1,54 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="shape" value="1" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/gamma"> gamma </csymbol>
-                <ci> shape </ci>
-                <cn type="integer"> 2 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.props
deleted file mode 100644
index 9adb52b..0000000
--- a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00099/00099-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = -0.897735417) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.sm
deleted file mode 100644
index 74a1254..0000000
--- a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.sm
+++ /dev/null
@@ -1,30 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00099/00099-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double truncationLowerBound = -Infinity; // 
-const double truncationUpperBound = 0.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.xml
deleted file mode 100644
index 4c74504..0000000
--- a/Benchmarks/SBMLstochasticTests/00099/00099-sbml-l3v2.xml
+++ /dev/null
@@ -1,57 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="truncationLowerBound" value="-INF" constant="true"/>
-      <parameter id="truncationUpperBound" value="0.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <cn type="integer"> 0 </cn>
-                <cn> 1.5 </cn>
-                <ci> truncationLowerBound </ci>
-                <ci> truncationUpperBound </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.props b/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.props
deleted file mode 100644
index d4b8798..0000000
--- a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.props
+++ /dev/null
@@ -1,5 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00100/00100-sbml-l3v2.xml
-// @GeneticLogicLab
-
-P=? [ true U [0,50] (X = 0) ]
\ No newline at end of file
diff --git a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.sm b/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.sm
deleted file mode 100644
index 3d928eb..0000000
--- a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.sm
+++ /dev/null
@@ -1,32 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/Benchmarks/SBML_Stochastic_Tests/00100/00100-sbml-l3v2.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double _C = 1.0;
-
-// Model parameters
-const double t = 0.0; // 
-const double mean = 0.0; // 
-const double stddev = 0.5; // 
-const double truncationLowerBound = -0.5; // 
-const double truncationUpperBound = 0.5; // 
-
-// Species _X
-module _X
-
-  _X  :  int init 0;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: _X
-rewards "_X" true : _X; endrewards
diff --git a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.xml b/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.xml
deleted file mode 100644
index 0ad040d..0000000
--- a/Benchmarks/SBMLstochasticTests/00100/00100-sbml-l3v2.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2" distrib:required="true">
-  <model>
-    <listOfCompartments>
-      <compartment id="C" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="X" compartment="C" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="t" value="0" constant="false"/>
-      <parameter id="mean" value="0" constant="true"/>
-      <parameter id="stddev" value="0.5" constant="true"/>
-      <parameter id="truncationLowerBound" value="-0.5" constant="true"/>
-      <parameter id="truncationUpperBound" value="0.5" constant="true"/>
-    </listOfParameters>
-    <listOfRules>
-      <rateRule variable="t">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <cn type="integer"> 1 </cn>
-        </math>
-      </rateRule>
-    </listOfRules>
-    <listOfEvents>
-      <event id="E0" useValuesFromTriggerTime="true">
-        <trigger initialValue="true" persistent="true">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <ci> t </ci>
-              <cn> 0.5 </cn>
-            </apply>
-          </math>
-        </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="X">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/distrib/normal"> normal </csymbol>
-                <ci> mean </ci>
-                <ci> stddev </ci>
-                <ci> truncationLowerBound </ci>
-                <ci> truncationUpperBound </ci>
-              </apply>
-            </math>
-          </eventAssignment>
-          <eventAssignment variable="t">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <apply>
-                <minus/>
-                <cn> 0.5 </cn>
-              </apply>
-            </math>
-          </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/ChemicalReactionNetworks/EnzymaticFutileCycle/results.txt b/ChemicalReactionNetworks/EnzymaticFutileCycle/results.txt
new file mode 100644
index 0000000..0e0d162
--- /dev/null
+++ b/ChemicalReactionNetworks/EnzymaticFutileCycle/results.txt
@@ -0,0 +1,2 @@
+0.0
+7.418844214740103E-4
diff --git a/ChemicalReactionNetworks/ReversibleIsomerization/results.txt b/ChemicalReactionNetworks/ReversibleIsomerization/results.txt
new file mode 100644
index 0000000..b2dc1ea
--- /dev/null
+++ b/ChemicalReactionNetworks/ReversibleIsomerization/results.txt
@@ -0,0 +1,2 @@
+0.0
+0.0
diff --git a/ChemicalReactionNetworks/SingleSpeciesProductionDegradation/results.txt b/ChemicalReactionNetworks/SingleSpeciesProductionDegradation/results.txt
new file mode 100644
index 0000000..63fa93f
--- /dev/null
+++ b/ChemicalReactionNetworks/SingleSpeciesProductionDegradation/results.txt
@@ -0,0 +1,2 @@
+0.0
+2.0523367282828658E-4
diff --git a/FaultTolerance/README.md b/FaultTolerance/README.md
deleted file mode 100644
index db151fc..0000000
--- a/FaultTolerance/README.md
+++ /dev/null
@@ -1,76 +0,0 @@
-# Fault Tolerance Computing and Electronics 
-
-This directory contains models in the fault tolerance domain. 
-
-At present there are two subdirectories containing 
-specialized models:
-
-```
-|-- Redundancy
-|   |-- RFB
-|   `-- TMR
-`-- StochasticComputing
-    |-- divide_by_two
-    `-- divider
-```
-
-An overview of each subcategory and the specific models is 
-provided in the text below. All of the provided cases are 
-designed to model transient noise or "soft" upsets, as opposed 
-to permanent hardware defects.
-
-
-# Redundancy Models
-
-Fault tolerant systems usually have redundant modules and/or signals 
-so that the system's correct function can be recovered, even in the 
-event of an error.
-
-## TMR: Triple Modular Redundancy
-
-This model represents a classic "majority vote" redundancy technique 
-that has been deployed in critical systems since the 1960s. The TMR
-model has a low state complexity and is provided mainly as a benchmark
-for judging the RFB model.
-
-## RFB: Restorative Feedback
-
-This model is an updated form of TMR designed to suppress transient 
-faults. RFB is also suitable for fault tolerance with non-binary 
-discrete signals as might be encountered in a data communication bus
-or high-density Flash memory. Due to its feedback dynamics and 
-non-binary signals, RFB can have a large or infinite state complexity.
-
-Two PRISM models are provided:
-
-* `rfb.pm` -- a binary-valued model with low state complexity.
-* `rfb_inf.pm` -- a multiple-valued model with infinite state complexity.
-
-
-# Stochastic Computing Models
-
-Fault tolerant systems sometimes employ "approximate" computing strategies 
-for masking or detecting errors in arithmetic or signal processing 
-circuits. Stochastic computing circuits operate by filtering pseudo-
-random bit-streams (PRBS) wherein the computation depends on the overall 
-average value rather than any particular bit. These circuits are therefore
-insensitive to a small number of transient upsets.
-
-## Divide-By-Two Circuit
-
-The stochastic divide-by-two function is based on the toggle flip-flop, 
-which provides a uniform output probability (i.e. average) independent 
-of the input probability. By using a simple feedback arrangement, this 
-property can be used to divide a PRBS value by 2.
-
-
-## Divider
-
-The divider circuit uses a counter to estimate a PRBS probability and 
-"re-emit" an independent PRBS with the same average value. The re-
-emitted stream is then used in feedback to obtain the ratio of two 
-PRBS averages. Two models are provided:
-
-* `divider.pm` -- a finite-state model with a fixed counter precision.
-* `divider_inf.pm` -- an infinite-state model with a variable counter precision.
-
diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/README.md b/FaultTolerance/Redundancy/RestorativeFeedback/README.md
deleted file mode 100644
index 895b310..0000000
--- a/FaultTolerance/Redundancy/RestorativeFeedback/README.md
+++ /dev/null
@@ -1,242 +0,0 @@
-# Restorative Feedback (RFB) Model
-
-This case example models a restorative feedback (RFB) circuit
-for in-situ transient error correction in logic circuits and
-systems. RFB can be classified as a type of Triple Modular
-Redundancy (TMR) wherein logic functions and signals are 
-instantiated in triplicate. Classical TMR systems use majority
-vote to correct a single error, but cannot detect or correct
-muliple errors. The RFB circuit is designed to correct momentary
-upsets with better reliability than Majority TMR. RFB is able
-to suppress multiple momentary faults when the feedback is
-active.
-
-There are two RFB models provided:
-
-* `rfb.pm` -- a PRISM model for a binary-valued RFB circuit with finite state complexity.
-  Properties are given in `rfb.props`.
-* `rfb_inf.pm` -- a PRISM model for a multiple-valued RFB circuit with infinite state complexity.
-  Properties are given in `rfb_inf.props`.
-
-
-## Description of the Binary RFB Circuit
-
-The RFB circuit is based on a modified Muller C-element gate. 
-The classical C-element is a binary-valued latch with behavior 
-described as 
-
-```
-if (A==B)
-  C = A;
-```
-
-When `A!=B` there is no change in `C`. 
-
-In the RFB circuit, the modified C-element has two modes depending 
-on an external clock. When the clock is low, the C-element is initialized
-to the value of an extra input `I`. When the clock is high, the C-element
-behaves as usual:
-
-```
-if (clk) begin
-  if (A==B) 
-     C = A;
-end else 
-  C = I;
-```
-
-![Modified Celement with initialization input.](../../../Media/ModifiedCElement.png)
-
-The RFB circuit shown below presumes that a logic system is replicated for a total 
-of three instances. Three logic signals x0, x1, and x2 represent instances
-the same logic value. Any of the signals may momentarily "flip" to an 
-erroneous value due to interference or noise. When the clock signal (not shown) 
-is low, the outputs y0, y1, and y2 are initialized to values sampled from 
-x1, x2, and x0, respectively.  When the clock is high, the C-element outputs
-are passed in a feedback cycle which corrects errors and suppresses further upsets.
-
-![RFB circuit.](../../../Media/RFBCircuit.png)
-
-To see how a single error is corrected, suppose x0 is initially in error, 
-so the input values are (x0,x1,x2)=(1,0,0). During the initialization, 
-the output values are set to (y0,y1,y2)=(x3,x1,x2)=(0,1,0). When the 
-clock swings high, the three C-elements see respective inputs (1,0), 
-(0,0) and (0,1). Since C2 sees inputs (0,0), its output is changed to 
-y2=0, so the outputs finally become (0,0,0) and the error is corrected.
-
-Reference:
-
-* Chris Winstead, Yi Luo, Eduardo Monzon, and Abiezer Tejeda, 
-  "An Error Correction Method for Binary and Multiple-Valued Logic",
-  *IEEE International Symposium on Multiple-Valued Logic*, 2011.
-* Chris Winstead, Yi Luo, Eduardo Monzon, and Abiezer Tejeda, 
-  "Error Correction via Restorative Feedback in M-ary Logic Circuits",
-  *J. of Multiple Valued Logic and Soft Computing*, Vol. 23, pp. 337, 2014.
-
-
-### PRISM Model for the Binary RFB Circuit
-
-The PRISM model for this circuit is provided in 
-`rfb.pm`. The input signals are assumed to be 0 (when correct),
-so a value of `1` indicates an error. The momentary upset rate
-is specified via constant `epsilon`, and the signal recovery rate
-is `Rc`. There is also a latch upset rate `alpha` which affects
-the C-element memory.
-
-For a C-element with inputs `A` and `B`, upsets are modeled as
-follows:
-
-* When `A=B`: not susceptible to state upsets.
-* When `A!=B`: susceptible to upset with rate `alpha`.
-
-The initial states are constrained by the integer
-constant named `initialErrors`, which indicates how
-many signal errors occur when the clock transitions from
-low to high. The PRISM model represents behavior during
-the correction phase, where the speed and ultimate error
-probability are determined by the circuit's feedback
-dynamics.
-
-Two example properties are given in `rfb.props`:
-
-* `P=? [ F[T,T] y1+y2+y3>1 ]`  evaluates the probability 
-that a non-correctable error state exists at time `T`. The
-constant `T` is a `double` indicating the elapsed time in
-the circuit's correction phase.
-* `S=? [ y1+y2+y3>1 ]` evaluates the steady-state probability
-that a non-correctable error state exists in the circuit's
-output.
-
-
-### Example results:
-
-The results given here are informative in comparison to the classical
-TMR model located in `../TMR`, demonstrating that RFB is more
-reliable for a system with the indicated parameters.
-
-
-#### `T=0`, `initialErrors=1`
-
-This case models the initial error probability before activating
-restorative feedback. Since there is initially only one error,
-we expect the timed property to be zero.
-
-```
-prism -const T=0 -const initialErrors=1 rfb.pm rfb.props
-```
-
-For the first property (at `T=0`) PRISM returns:
-
-```
-Result: [0.0,0.0]
-```
-
-For the second property (steady state) PRISM returns:
-
-```
-Result: [1.272254163993728E-6,1.272254163993728E-6]
-```
-
-#### `T=1.0`, `initialErrors=1`
-
-This case models the error probability 1.0 time units after
-activating restorative feedback. This case provides
-information about the circuit's transient reliability.
-
-```
-prism -const T=1.0 -const initialErrors=1 rfb.pm rfb.props
-```
-
-For the first property (at `T=0`) PRISM returns:
-
-```
-Result: [4.3735439267849973E-4,4.3735439267849984E-4]
-```
-
-For the second property (steady state) PRISM returns:
-
-```
-Result: [1.272254163993728E-6,1.272254163993728E-6]
-```
-
-
-## Description of the Multiple-Valued RFB Circuit
-
-One of the motivations for the RFB method is to apply TMR 
-to systems with non-binary signals. Classical TMR relies on 
-Majority logic that requires two of the three signals be 
-equal. In systems with multiple-valued signals, all three 
-signals may differ, so there is no majority. In that situation, 
-the C-element's latching behavior provides a solution.
-
-The multiple-valued C-Element and RFB circuit have the same 
-design as the binary case, except that the signals are allowed 
-to be arbitrary discrete levels. The upset processes are now 
-also multiple-valued, requiring more complex models.
-
-
-### PRISM Model for the Multiple-Valued RFB Circuit
-
-The PRISM model for this circuit is provided in 
-`rfb_inf.pm`. The input signals are assumed to be 0 (when correct).
-The momentary upset rate is specified via constant `epsilon`, and 
-the signal recovery rate is `Rc`. Since the signal values are non-binary, 
-the upset amplitude is modeled by a "noise" signal with rate `Rn`. 
-The noise amplitude distribution is:
-
-* n=1 with rate `Rn`
-* n=2 with rate `Rn/2`
-* n=3 with rate `Rn/4`
-* n=4 with rate `Rn/8`
-
-This example noise process is not based on any specific physical model, 
-but is similar to "random telegraph noise" known to affect various FET 
-and memristor devices.
-
-There is also a latch upset rate `alpha` which affects the C-element memory.
-Here the latch upset is identical to the binary-valued circuit. Latch upsets
-always have amplitude 1, i.e. the C-element output drifts to an adjacent 
-signal level.
-
-Initial values for this model are given explicitly via integer constants 
-`i1`, `i2`, and `i3`, so a single initial state is specified (the binary-
-valued circuit allowed specifying an ensemble of initial states, but that 
-is not possible here).
-
-Property definitions are more challenging for the multiple-valued circuit
-compared to the binary case. Steady-state properties are not available 
-due to the model's unbounded state complexity. One property is provided 
-in `rfb_inf.props`:
-
-* `P=? [ F[T,T] y1+y2+y3!=0 ]`
-
-This evaluates the probability that the output signals are error-free at 
-time `T`. 
-
-### Example Results for the Multiple-Valued Circuit
-
-#### `i1=0`, `i2=3`, `i3=1`, `T=20`
-
-```
-prism -sim -const i1=0 -const i2=3 -const i3=1 -const T=20 rfb_inf.pm rfb_inf.props
-```
-
-The result reported by PRISM is
-
-```
-Result: 0.051 (+/- 0.017928853962181267 with probability 0.99; rel err 0.3515461561212013)
-```
-
-
-#### `i1=0`, `i2=0`, `i3=1`, `T=20`
-
-```
-prism -sim -const i1=0 -const i2=0 -const i3=1 -const T=20 rfb_inf.pm rfb_inf.props
-```
-
-The result reported by PRISM is
-
-```
-Result: 0.024 (+/- 0.012472826037899055 with probability 0.99; rel err 0.5197010849124606)
-```
-
diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.pm b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.pm
deleted file mode 100644
index a421d29..0000000
--- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.pm
+++ /dev/null
@@ -1,49 +0,0 @@
-// rfb.pm
-// Restorative Feedback model
-// A type of Triple Modular Redundancy (TMR)
-ctmc
-
-const double Rc      = 10;       // signal transition rate of logic gates
-const double Rn      = 2;        // noise process rate
-const double epsilon = 1;        // transient upset rate
-const double alpha   = .1;       // state upset rate
-const double T;
-const int    i1;
-const int    i2;
-const int    i3;
-
-
-// Noise sources
-module noise1
-  n1: int init 0;
-
-  [] (true) -> Rn:(n1'=1)+(Rn/2):(n1'=2)+(Rn/4):(n1'=3)+(Rn/8):(n1'=4);
-endmodule
-module noise2 = noise1 [ n1=n2 ] endmodule
-module noise3 = noise1 [ n1=n3 ] endmodule
-
-
-// Signal Source
-module source1 
-  x1 : int init i1;
-
-  []  (x1 > 0) -> (epsilon/2):(x1'=x1+n1) + (epsilon/2):(x1'=x1-n1) + Rc:(x1'=x1-1);
-  []  (x1 = 0) -> (epsilon/2):(x1'=x1+n1) + (epsilon/2):(x1'=x1-n1);
-  []  (x1 < 0) -> (epsilon/2):(x1'=x1+n1) + (epsilon/2):(x1'=x1-n1) + Rc:(x1'=x1+1);
-endmodule
-
-module source2 = source1 [ x1=x2, i1=i2, n1=n2 ] endmodule
-module source3 = source1 [ x1=x3, i1=i3, n1=n3 ] endmodule
-
-
-// Modified Muller C-element
-module Cem1
-  y1 : int init i3;
-
-  [] (x1 = y3)  -> (Rc):(y1' = y3);
-  [] (x1 != y3) -> (alpha/2):(y1'=y1+1)+(alpha/2):(y1'=y1-1);
-endmodule
-
-module Cem2 = Cem1 [ x1=x2, y1=y2, y3=y1, i3 = i1 ] endmodule
-module Cem3 = Cem1 [ x1=x3, y1=y3, y3=y2, i3 = i2 ] endmodule
-
diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.props b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.props
deleted file mode 100644
index 7228516..0000000
--- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback.props
+++ /dev/null
@@ -1 +0,0 @@
-P=? [ F[T,T] y1+y2+y3!=0 ]
diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.pm b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.pm
deleted file mode 100644
index 34858c1..0000000
--- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.pm
+++ /dev/null
@@ -1,35 +0,0 @@
-// rfb.pm
-// Restorative Feedback model
-// A type of Triple Modular Redundancy (TMR)
-ctmc
-
-const double Rc      =100;     // signal transition rate of logic gates
-const double epsilon =1;       // transient upset rate
-const double alpha   =0.01;    // state upset rate
-const double T;
-const int    initialErrors;
-
-// Signal Source
-module source1 
-  x1 : [0..1];
-
-  []  (true) -> epsilon:(x1'=1) + Rc:(x1'=0);
-endmodule
-
-module source2 = source1 [x1=x2] endmodule
-module source3 = source1 [x1=x3] endmodule
-
-
-// Modified Muller C-element
-module Cem1
-  y1 : [0..1];
-
-  [] (x1 = y3)  -> (Rc):(y1' = y3);
-  [] (x1 != y3) -> (alpha):(y1'=1-y1);
-endmodule
-
-module Cem2 = Cem1 [y1=y2, x1=x2, y3=y1] endmodule
-module Cem3 = Cem1 [y1=y3, x1=x3, y3=y2] endmodule
-
- 
-init ((x1+x2+x3=initialErrors) & ((y1=x3)&(y2=x1)&(y3=x2))) endinit
diff --git a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.props b/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.props
deleted file mode 100644
index c72acba..0000000
--- a/FaultTolerance/Redundancy/RestorativeFeedback/RestorativeFeedback_bound.props
+++ /dev/null
@@ -1,2 +0,0 @@
-P=? [ F[T,T] y1+y2+y3>1 ]
-S=? [ y1+y2+y3>1 ]
\ No newline at end of file
diff --git a/FaultTolerance/Redundancy/TripleModularRedundancy/README.md b/FaultTolerance/Redundancy/TripleModularRedundancy/README.md
deleted file mode 100644
index 4184f47..0000000
--- a/FaultTolerance/Redundancy/TripleModularRedundancy/README.md
+++ /dev/null
@@ -1,100 +0,0 @@
-# Triple Modular Redundancy (TMR) Model
-
-This case example models a Triple Modular Redundancy (TMR) circuit
-wherein logic functions and signals are instantiated in triplicate. 
-Logic states are corrected using majority vote modules, so that a 
-single error can be corrected. In this model we assume that all signals
-are susceptible to momentary upsets, including the majority outputs.
-
-
-## Description of the Circuit
-
-
-The TMR circuit shown below presumes that a logic system is replicated for a total 
-of three instances. Three logic signals x0, x1, and x2 represent instances
-the same logic value. Any of the signals may momentarily "flip" to an 
-erroneous value due to interference or noise. The majority gates labeled `M`
-output the majority decision among the three input signals. Since the majority 
-gates may also be susceptible to upsets, there are three independent majority 
-gates so that there is never a single point of failure.
-
-![Majority TMR circuit.](../../../Media/MajorityTMR.png)
-
-Reference:
-
-* R. E. Lyons and W. Vanderkulk, "The use of triple-modular redundancy to improve
-computer reliability." *IBM Journal of Research and Development*, 6(2):200, 1962.
-
-## PRISM Model
-
-The PRISM model for this circuit is provided in 
-`tmr.pm`. The input signals are assumed to be 0 (when correct),
-so a value of `1` indicates an error. The momentary upset rate
-is specified via constant `epsilon`, and the signal recovery rate
-is `Rc`. 
-
-The initial states are constrained by the integer
-constant named `initialErrors`, which indicates how
-many signal errors are present in the initial state.
-
-Two example properties are given in `tmr.props`:
-
-* `P=? [ F[T,T] y1+y2+y3>1 ]`  evaluates the probability 
-that a non-correctable error state exists at time `T`. The
-constant `T` is a `double` indicating the elapsed time.
-* `S=? [ y1+y2+y3>1 ]` evaluates the steady-state probability
-that a non-correctable error state exists in the circuit's
-output.
-
-The TMR's output error probability is not strongly dependent on 
-time, so these two properties should usually be close to each other.
-
-
-## Example results:
-
-
-### `T=0`, `initialErrors=1`
-
-This case models the initial error probability. Since the majority 
-gates have undefined (or unconstrained) initial output values, 
-the instantaneous error probability is indeteminate. 
-
-```
-prism -const T=0 -const initialErrors=1 tmr.pm tmr.props
-```
-
-For the first property (at `T=0`) PRISM returns:
-
-```
-Result: [0.0,1.0]
-```
-
-For the second property (steady state) PRISM returns:
-
-```
-Result: [4.94427886688858E-4,4.94427886688858E-4]
-```
-
-### `T=1.0`, `initialErrors=1`
-
-This case models the error probability after 1.0 time units.
-Since this is well beyond the mean signal recovery time `1/Rc`,
-the transient error probability should be nearly equal to the steady
-state.
-
-```
-prism -const T=1.0 -const initialErrors=1 tmr.pm tmr.props
-```
-
-For the first property (at `T=0`) PRISM returns:
-
-```
-Result: [4.944279220969286E-4,4.94427973657968E-4]
-```
-
-For the second property (steady state) PRISM returns:
-
-```
-Result: [4.94427886688858E-4,4.94427886688858E-4]
-```
-
diff --git a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.pm b/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.pm
deleted file mode 100644
index 69b9e8e..0000000
--- a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.pm
+++ /dev/null
@@ -1,35 +0,0 @@
-// tmr.pm
-// Triple Modular Reduncancy model
-// using majority logic
-ctmc
-
-const double Rc=100;          // signal transition rate of logic gates
-const double epsilon=1;       // transient upset rate
-const double T;
-const int    initialErrors;
-
-// Signal Source
-module source1 
-  x1 : [0..1];
-
-  []  (true) -> epsilon:(x1'=1) + Rc:(x1'=0);
-endmodule
-
-module source2 = source1 [x1=x2] endmodule
-module source3 = source1 [x1=x3] endmodule
-
-
-// Majority Gates
-module Maj1
-  y1 : [0..1];
-
-  [] (x1 + x2 + x3 > 1)  -> (Rc):(y1' = 1) + epsilon:(y1'=0);
-  [] (x1 + x2 + x3 < 2)  -> (Rc):(y1' = 0) + epsilon:(y1'=1);
-
-endmodule
-
-module Maj2 = Maj1 [y1=y2] endmodule
-module Maj3 = Maj1 [y1=y3] endmodule
-
- 
-init (x1+x2+x3=initialErrors) endinit
diff --git a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.props b/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.props
deleted file mode 100644
index c72acba..0000000
--- a/FaultTolerance/Redundancy/TripleModularRedundancy/TripleModularRedundancy.props
+++ /dev/null
@@ -1,2 +0,0 @@
-P=? [ F[T,T] y1+y2+y3>1 ]
-S=? [ y1+y2+y3>1 ]
\ No newline at end of file
diff --git a/FaultTolerance/StochasticComputing/divide_by_two/README.md b/FaultTolerance/StochasticComputing/divide_by_two/README.md
deleted file mode 100644
index 0107305..0000000
--- a/FaultTolerance/StochasticComputing/divide_by_two/README.md
+++ /dev/null
@@ -1,76 +0,0 @@
-# Unipolar Stochastic Divide-By-Two Model
-
-This case example models a stochastic divide-by-two circuit 
-using the unipolar stochastic numerical format. In the 
-unipolar format, a signal $x$ is a real number between 
-0 and 1, encoded probabilistically in a binary signal 
-$X(t)$. At any time $t$, the signal $X(t)=1$ with 
-probability $x$, and $X(t)=0$ with probability $1-x$.
-
-## Description of the Circuit
-
-The divide-by-two circuit schematic is shown below. It accepts 
-one stochastic input, $A(t)$, and produces a single output $Q(t)$. 
-Ideally $Q$ should arrive at a steady-state probability $q=a/2$. 
-
-![Unary divide-by-two schematic](../../../Media/StochasticDivideByTwo.png)
-
-The principle of operation is as follows. The toggle flip-flop
-emits a bitstream $B(t)$ with steady-state probability $b=1/2$, 
-independent of the input stream probability. The AND gate acts as 
-a probability multiplier, so it emits a bitstream with probability 
-$q=ab=q/2$. 
-
-Reference:
-
-* C. Winstead, "Tutorial on Stochastic Computation," 
-  Chapter 2 in *Stochastic Computing: Techniques and Applications*, 
-  ed. Gaudet and Gross, Springer, 2019.
-
-
-## PRISM Model
-
-The PRISM model for this circuit is provided in 
-`divide_by_two.pm`. The input probability is given 
-via the constant `a`. Internally, the stochastic 
-input signal is `inA`, and the output signal is `Q`.
-
-Three example properties are given in `divide_by_two.props`:
-
-* `P=? [ F[T,T] Q = 1 ]`  evaluates the probability 
-that Q=1 (i.e. the numerical output $q$) at `T` clock cycles, 
-which relates to the circuit's response time. The constant `T`
-is an integer.
-* `S=? [ Q = 1 ]` evaluates the steady-state probability
-that Q=1. 
-* `P=? [ F[T,T] Q = 1 ] - S=? [ Q = 1 ]` evaluates the transient
-absolute error in output probability at clock cycle `T`.
-
-## Example results:
-
-### `a=0.1` and `T=100` 
-
-The expected output is $q=0.05$. 
-
-```
-prism --const a=0.1 --const T=100 divide_by_two.pm divide_by_two.props
-```
-
-For the first property (at 100 clock cycles) PRISM returns:
-
-```
-Result: 0.049999999984085816 (exact floating point)
-```
-
-For the second property (steady state) PRISM returns:
-
-```
-Result: 0.04999998765587841
-```
-
-For the third property (transient error) PRISM returns:
-
-```
-Result: 1.2328207406320235E-8
-```
-
diff --git a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.pm b/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.pm
deleted file mode 100644
index 03164a2..0000000
--- a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.pm
+++ /dev/null
@@ -1,39 +0,0 @@
-// divide_by_two.pm
-// Unipolar Stochastic Divide-By-2
-// Based on Toggle Flip-Flop
-
-dtmc
-
-const double a;  // input value between 0 and 1
-const int T;     // clock cycle count
-
-//------------------
-// Signal Sources
-//------------------
-module Source0
-  inA : [0..1] init 0;
-
-  [event] (true) -> a:(inA'=1) + (1-a):(inA'=0);
-endmodule
-
-//------------------------
-// Toggle Flip-Flop (TFF)
-//------------------------
-module TFF
-   B : [0..1] init 0;
-  
-   [event] (inA=0) -> (B' = B);
-   [event] (inA=1) -> (B' = 1-B);
-endmodule
-
-
-//------------------
-// AND gate
-//------------------
-module AND0
-
-  Q : [0..1] init 0;
-  
-  [event] (inA=1 & B=1)  -> (Q'=1);
-  [event] (inA=0 | B=0)  -> (Q'=0);  
-endmodule
diff --git a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.props b/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.props
deleted file mode 100644
index cf2de91..0000000
--- a/FaultTolerance/StochasticComputing/divide_by_two/divide_by_two.props
+++ /dev/null
@@ -1,5 +0,0 @@
-P=? [ F[T,T] Q=1 ]
-
-S=? [ Q=1 ]
-
-(P=? [ F[T,T] Q=1 ]) - (S=? [ Q=1 ])
diff --git a/FaultTolerance/StochasticComputing/divider/README.md b/FaultTolerance/StochasticComputing/divider/README.md
deleted file mode 100644
index 5fd2591..0000000
--- a/FaultTolerance/StochasticComputing/divider/README.md
+++ /dev/null
@@ -1,126 +0,0 @@
-# Unipolar Stochastic Divider Model
-
-This case example models a stochastic divider using 
-the unipolar stochastic numerical format. In the 
-unipolar format, a signal $x$ is a real number between 
-0 and 1, encoded probabilistically in a binary signal 
-$X(t)$. At any time $t$, the signal $X(t)=1$ with 
-probability $x$, and $X(t)=0$ with probability $1-x$.
-
-Two models are provided:
-
-* `divider.pm` is a finite-state model.
-* `divider_inf.pm` is an intinite-state model.
-
-Both models rely on a finite up-down counter to 
-estimate the average probability of a unary stochastic 
-bitstream. The finite counter saturates at `MAX_COUNT`, 
-which is a fixed constant in the model.
-
-In the infinite-state model, the counter's limit is 
-variable, initially +/-1 and increasing logarithmically
-with respect to the elapsed clock cycles. This approach 
-improves accuracy for calculations with small probabilities,
-e.g. below 0.01, however the state complexity becomes 
-unbounded in this model.
-
-
-## Description of the Circuit
-
-The divider circuit shematic is shown below. It accepts 
-two stochastic inputs, $A(t)$ and $B(t)$, and produces a 
-single output $Q(t)$. Ideally $Q$ should arrive at a 
-steady-state probability $Q(t)=q=a/b$. 
-
-![Unary divider schematic](../../../Media/StochasticUnaryDivider.png)
-
-The principle of operation is as follows. The signed up/down
-counter (UDC) reaches equilibrium when its inputs have equal 
-probability. The module R emits a bit stream with probability 
-equal to the counter value C, scaled to the range (0,1).
-The AND gate acts as a probability multiplier, so it emits bits 
-with probability $qb$. Due to the feedback connection, at 
-steady state we expect $qb=a$ and therefore $q=a/b$.
-
-Reference:
-
-* C. Winstead, "Tutorial on Stochastic Computation," 
-  Chapter 2 in *Stochastic Computing: Techniques and Applications*, 
-  ed. Gaudet and Gross, Springer, 2019.
-
-
-## PRISM Model
-
-The input probabilities are given via constants `a` and `b`. Internally, 
-the stochastic input signals are `inA` and `inB`, and the output 
-signal is `Q`.
-
-Two example properties are given in `divider.props`:
-
-* `P=? [ F[T,T] Q = 1 ]`  evaluates the probability 
-that Q=1 (i.e. the numerical output $q$) at `T` clock cycles, 
-which relates to the circuit's response time. The constant `T`
-is an integer.
-* `S=? [ Q = 1 ]` evaluates the steady-state probability
-that Q=1. 
-
-## Example results (finite state model):
-
-### `a=0.1`, `b=0.3`, and `T=100` 
-
-The expected output is $q=1/3$. 
-
-```
-prism --const a=0.1 --const b=0.3 --const T=100 divider.pm divider.props
-```
-
-For the first property (at 100 clock cycles) PRISM returns:
-
-```
-Result: 0.4665562152140168 (exact floating point)
-```
-
-For the second property (steady state) PRISM returns:
-
-```
-Result: 0.33333443639168
-```
-
-
-### `a=0.7`, `b=0.3`, and `T=100` 
-
-In this case the ratio $a/b$ is greather than one, so the expected output 
-is saturated close to $q=1$. 
-
-```
-prism --const a=0.1 --const b=0.3 --const T=100 divider.pm divider.props
-```
-
-For the first property (at 100 clock cycles) PRISM returns:
-
-```
-Result: 0.8790749994268042 (exact floating point)
-```
-
-For the second property (steady state) PRISM returns:
-
-```
-Result: 0.9881554646304057
-```
-
-
-## Example results (infinite state model):
-
-### `a=0.001`, `b=0.1`
-
-In this case PRISM is best used to simulate a path with 
-10,000 clock cycles. The output bitstream `Q` is reported in 
-column 9 of the output trace.
-
-```
-prism -simpath time=10000 data -const a=0.001 -const b=0.1 -const T=1000 divider_inf.pm
-```
-
-In this model PRISM is unable to provide the requested path length,
-so it is not possible to compute the long-term transient behavior 
-or the steady-state output probability using PRISM.
diff --git a/FaultTolerance/StochasticComputing/divider/divider.pm b/FaultTolerance/StochasticComputing/divider/divider.pm
deleted file mode 100644
index fde5be1..0000000
--- a/FaultTolerance/StochasticComputing/divider/divider.pm
+++ /dev/null
@@ -1,49 +0,0 @@
-// Unipolar stochastic divider circuit  
-dtmc
-
-const double a;
-const double b;
-const int T;
-
-// Saturation level for up-down counter
-const int MAXCOUNT=63;
-
-//------------------
-// Signal Sources
-//------------------
-module Source0
-  inA : [0..1] init 0;
-
-  [event] (inA=0 | inA=1) -> a:(inA'=1) + (1-a):(inA'=0);
-endmodule
-
-// Second signal source:
-module Source1 = Source0 [ inA=inB, a=b ] endmodule
-
-
-// AND gate
-module AND0
-  QB : [0..1] init 0;
-
-  [event] (inB=1)&(Q=1)  ->  (QB' = 1);
-  [event] !(inB=1 & Q=1) ->  (QB' = 0);
-endmodule
-
-
-// Up-Down Counter
-module UDC0
-   c0: [-MAXCOUNT..MAXCOUNT] init 0;
-
-   [event] (c0 > -MAXCOUNT) & (c0 < MAXCOUNT) -> 1:(c0' = c0 + inA - QB);
-   [event] (c0 = -MAXCOUNT) -> 1:(c0' = c0 + inA);
-   [event] (c0 = MAXCOUNT)  -> 1:(c0' = c0 - QB);  
-endmodule
-
-// Output and Feedback
-formula q=(c0+MAXCOUNT+1)/(2*(MAXCOUNT+1));
-module FB0
-   Q: [0..1] init 0;
-
-   [event]  (c0 >= -MAXCOUNT) & (c0 <= MAXCOUNT) ->  q:(Q' = 1) + (1-q):(Q'=0); 
-endmodule
-
diff --git a/FaultTolerance/StochasticComputing/divider/divider.props b/FaultTolerance/StochasticComputing/divider/divider.props
deleted file mode 100644
index 7ab1358..0000000
--- a/FaultTolerance/StochasticComputing/divider/divider.props
+++ /dev/null
@@ -1,4 +0,0 @@
-P=? [ F[T,T] Q = 1 ]
-
-S=? [ Q = 1 ]
-
diff --git a/FaultTolerance/StochasticComputing/divider/divider_inf.pm b/FaultTolerance/StochasticComputing/divider/divider_inf.pm
deleted file mode 100644
index 40b24bd..0000000
--- a/FaultTolerance/StochasticComputing/divider/divider_inf.pm
+++ /dev/null
@@ -1,54 +0,0 @@
-// Unipolar stochastic divider circuit  
-dtmc
-
-const double a;
-const double b;
-const int    T;
-
-//------------------
-// Signal Sources
-//------------------
-module Source0
-  inA : [0..1] init 0;
-
-  [event] (inA=0 | inA=1) -> a:(inA'=1) + (1-a):(inA'=0);
-endmodule
-
-// Second signal source:
-module Source1 = Source0 [ inA=inB, a=b ] endmodule
-
-
-// AND gate
-module AND0
-  QB : [0..1] init 0;
-
-  [event] (inB=1)&(Q=1)  ->  (QB' = 1);
-  [event] !(inB=1 & Q=1) ->  (QB' = 0);
-endmodule
-
-
-// Up-Down Counter
-module UDC0
-   c0: int init 0;
-
-   [event] (true) -> 1:(c0' = c0 + inA - QB);
-endmodule
-
-// Clock Timer
-module clockTimer
-   N: int init 1;
-   M: int init 1;
-
-   [event] (true) -> 1:(N'=N+1)&(M'=1+round(log(N,2)));
-endmodule
-
-
-// Output and Feedback
-formula q=(c0+M+1)/(2*(M+1));
-module FB0
-   Q: [0..1] init 0;
-
-   [event]  (c0 >= -M) & (c0 <= M) ->  q:(Q' = 1) + (1-q):(Q'=0); 
-
-endmodule
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.props
similarity index 77%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.props
index d0b751b..46cde8a 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.csl
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.props
@@ -1,6 +1,3 @@
 // Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
 
 P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml
index a4429d7..27aed86 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="300"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="159" layout:y="380"/>
-                      <layout:end layout:x="145" layout:y="320"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="38" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="187" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="126" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="227" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="121" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="95" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="30"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="115" layout:y="290"/>
-                      <layout:end layout:x="30" layout:y="40"/>
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-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="40" layout:y="60"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
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-                      <layout:end layout:x="50" layout:y="70"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="90"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
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-                      <layout:end layout:x="70" layout:y="100"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BetI_degradation_interaction" layout:reaction="BetI_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="120"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BetI_degradation_interaction__substrate__BetI_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BetI_protein">
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-                      <layout:end layout:x="90" layout:y="130"/>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="150"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
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-                      <layout:start layout:x="40" layout:y="200"/>
-                      <layout:end layout:x="110" layout:y="160"/>
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-              </layout:speciesReferenceGlyph>
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-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__repression__AmtR_protein">
-            <layout:boundingBox>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Ara_AraC_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
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-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="88" layout:y="20"/>
-                      <layout:end layout:x="40" layout:y="200"/>
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-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__AmtR_protein">
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-              <layout:position layout:x="40" layout:y="200"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
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-                  <layout:listOfCurveSegments>
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-                      <layout:end layout:x="40" layout:y="200"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_protein__repression__YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="159" layout:y="380"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__PhlF_protein__repression__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="115" layout:y="290"/>
-                      <layout:end layout:x="159" layout:y="380"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BetI_protein__repression__YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="159" layout:y="380"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
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-                      <layout:end layout:x="159" layout:y="380"/>
-                    </layout:curveSegment>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="247" layout:y="200"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
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-                      <layout:end layout:x="247" layout:y="200"/>
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-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__BetI_protein">
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-            <layout:listOfSpeciesReferenceGlyphs>
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-            <layout:listOfSpeciesReferenceGlyphs>
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                   <rdf:Bag>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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                   <rdf:Bag>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/>
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                   <rdf:Seq>
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+                </mts:DNAComponents>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
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+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                <mts:Strand>+</mts:Strand>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pTet" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                </mts:ComponentDefinitions>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <gt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
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               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
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+                  </rdf:Description>
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+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
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+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
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@@ -1334,11 +1208,8 @@
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-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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+                  <times/>
                   <apply>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
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+                  <ci> topModel_YFPpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
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+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
-                    </modifierSpeciesReference>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
               </apply>
             </apply>
           </math>
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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                 <mts:Interactions>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1625,11 +1553,8 @@
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                   <apply>
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
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+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml
index a4429d7..27aed86 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_000to011_G1_10_10.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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                   <rdf:Seq>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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                   <rdf:Bag>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pTet" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
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         </annotation>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:FunctionalComponents>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <gt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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@@ -1140,11 +978,8 @@
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-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
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                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
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-                  <cn type="integer"> 1 </cn>
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-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
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+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
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@@ -1182,52 +1014,76 @@
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+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
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@@ -1237,11 +1093,8 @@
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
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+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
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+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
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@@ -1334,11 +1208,8 @@
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-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
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               <apply>
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+                  <times/>
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-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
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-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
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@@ -1376,52 +1244,76 @@
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
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             </apply>
           </math>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
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+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
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-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
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             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1625,11 +1553,8 @@
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
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                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.props
similarity index 77%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.props
index d0b751b..46cde8a 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_G1.csl
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.props
@@ -1,6 +1,3 @@
 // Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
 
 P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1/Circuit0x8E_000to011.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1/Circuit0x8E_000to101.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10/Circuit0x8E_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1/Circuit0x8E_000to101.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10/Circuit0x8E_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10/Circuit0x8E_G1.csl
deleted file mode 100644
index a87d3b7..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10/Circuit0x8E_G1.csl
+++ /dev/null
@@ -1,3 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein < 30) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10/Circuit0x8E_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10/Circuit0x8E_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl
deleted file mode 100644
index a87d3b7..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl
+++ /dev/null
@@ -1,3 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein < 30) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1/Circuit0x8E_000to101.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1/Circuit0x8E_000to101.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_000to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml
index 8ec5919..a55b6e2 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0/Circuit0x8E_010to100.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="300"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="159" layout:y="380"/>
-                      <layout:end layout:x="145" layout:y="320"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="38" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="187" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="126" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="227" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="121" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="95" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="30"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="115" layout:y="290"/>
-                      <layout:end layout:x="30" layout:y="40"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="40" layout:y="60"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__YFP_degradation_interaction__substrate__YFP_protein" layout:role="substrate" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="159" layout:y="380"/>
-                      <layout:end layout:x="50" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="90"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="141" layout:y="110"/>
-                      <layout:end layout:x="70" layout:y="100"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BetI_degradation_interaction" layout:reaction="BetI_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="120"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BetI_degradation_interaction__substrate__BetI_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BetI_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="247" layout:y="200"/>
-                      <layout:end layout:x="90" layout:y="130"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="150"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="40" layout:y="200"/>
-                      <layout:end layout:x="110" layout:y="160"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__repression__AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="40" layout:y="200"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Ara_AraC_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="88" layout:y="20"/>
-                      <layout:end layout:x="40" layout:y="200"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="40" layout:y="200"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="141" layout:y="110"/>
-                      <layout:end layout:x="40" layout:y="200"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_protein__repression__YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="159" layout:y="380"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__PhlF_protein__repression__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="115" layout:y="290"/>
-                      <layout:end layout:x="159" layout:y="380"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BetI_protein__repression__YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="159" layout:y="380"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__BetI_protein__repression__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="247" layout:y="200"/>
-                      <layout:end layout:x="159" layout:y="380"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="247" layout:y="200"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="141" layout:y="110"/>
-                      <layout:end layout:x="247" layout:y="200"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="247" layout:y="200"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR_protein__repression__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="207" layout:y="20"/>
-                      <layout:end layout:x="247" layout:y="200"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__LacI_protein__repression__PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="290"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI_protein__repression__PhlF_protein" layout:role="product" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="146" layout:y="200"/>
-                      <layout:end layout:x="115" layout:y="290"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_protein__repression__PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="290"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__AmtR_protein__repression__PhlF_protein" layout:role="product" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="40" layout:y="200"/>
-                      <layout:end layout:x="115" layout:y="290"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__repression__HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="141" layout:y="110"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Ara_AraC_protein__repression__HlyIIR_protein" layout:role="product" layout:speciesGlyph="Glyph__HlyIIR_protein">
-                <layout:curve>
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-                      <layout:start layout:x="88" layout:y="20"/>
-                      <layout:end layout:x="141" layout:y="110"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="141" layout:y="110"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
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-                <layout:curve>
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-          </layout:reactionGlyph>
-        </layout:listOfReactionGlyphs>
-        <layout:listOfTextGlyphs>
-          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__AmtR_protein" layout:id="TextGlyph__AmtR_protein" layout:text="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__Ara_AraC_protein" layout:id="TextGlyph__Ara_AraC_protein" layout:text="Ara_AraC_protein">
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                   <rdf:Bag>
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+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                <mts:Strand>+</mts:Strand>
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+          </ModelToSBOL>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
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+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim8">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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+              </ModelToSBOL>
             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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+                </rdf:RDF>
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             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
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+                    </mts:Participations>
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@@ -1334,11 +1208,8 @@
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-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
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+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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-        <listOfModifiers>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
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@@ -1431,11 +1323,8 @@
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-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
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                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
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                 <plus/>
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                 <apply>
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-                  <cn type="integer"> 1 </cn>
+                  <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
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+                </mts:Interactions>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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@@ -1528,11 +1438,8 @@
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
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@@ -1625,11 +1553,8 @@
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-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
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+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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+                  <times/>
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-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
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@@ -1667,52 +1589,76 @@
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+        <addedPrefix:listOfProducts>
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                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml
index 8ec5919..a55b6e2 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_010to100_G0_10_10.xml
@@ -1,786 +1,535 @@
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                   <rdf:Bag>
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+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
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-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
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         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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                     <mts:Participations>
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim8">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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@@ -1334,11 +1208,8 @@
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
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+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1625,11 +1553,8 @@
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                   <apply>
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10/Circuit0x8E_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_010to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml
index 759239c..e420e64 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0/Circuit0x8E_010to111.xml
@@ -1,785 +1,535 @@
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                   <rdf:Bag>
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+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+            </rdf:RDF>
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         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
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-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -787,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -819,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -850,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -881,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -912,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -943,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1013,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1043,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1084,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1139,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1152,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1181,52 +1014,76 @@
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             </apply>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1236,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1249,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1278,52 +1129,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1333,11 +1208,8 @@
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1346,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1375,52 +1244,76 @@
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
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+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1430,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1443,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1472,52 +1359,76 @@
               </apply>
             </apply>
           </math>
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-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1527,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1540,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1569,52 +1474,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1624,11 +1553,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1637,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1666,52 +1589,76 @@
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
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             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1721,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1734,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1763,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1833,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1863,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1904,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1959,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1972,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2001,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml
index 759239c..e420e64 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_010to111_G0_10_10.xml
@@ -1,785 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="300"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
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+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+            </rdf:RDF>
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         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
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-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
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-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -787,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -819,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -850,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -881,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -912,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -943,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1013,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1043,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1084,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1139,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1152,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1181,52 +1014,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1236,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1249,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1278,52 +1129,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1333,11 +1208,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1346,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1375,52 +1244,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1430,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1443,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1472,52 +1359,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1527,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1540,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1569,52 +1474,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1624,11 +1553,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1637,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1666,52 +1589,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1721,11 +1668,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1734,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1763,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1833,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1863,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1904,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1959,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1972,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2001,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10/Circuit0x8E_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_010to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1/Circuit0x8E_011to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1/Circuit0x8E_011to000.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1/Circuit0x8E_011to000.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1/Circuit0x8E_011to000.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10/Circuit0x8E_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10/Circuit0x8E_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10/Circuit0x8E_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10/Circuit0x8E_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_011to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1/Circuit0x8E_011to101.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1/Circuit0x8E_011to101.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1/Circuit0x8E_011to101.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1/Circuit0x8E_011to101.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10/Circuit0x8E_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10/Circuit0x8E_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10/Circuit0x8E_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10/Circuit0x8E_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_011to101_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml
index fc292cb..2b5878a 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0/Circuit0x8E_100to010.xml
@@ -1,786 +1,535 @@
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         </annotation>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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                   <rdf:Bag>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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                   <rdf:Seq>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
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                   <rdf:Seq>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
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         </annotation>
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+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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                   <rdf:Bag>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                </mts:DNAComponents>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pTet" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:ComponentDefinitions>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
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               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
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+                  </rdf:Description>
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+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
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+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
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@@ -1334,11 +1208,8 @@
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-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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+                  <times/>
                   <apply>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
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+                  <ci> topModel_YFPpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
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+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
-                    </modifierSpeciesReference>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
               </apply>
             </apply>
           </math>
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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                 <mts:Interactions>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1625,11 +1553,8 @@
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                   <apply>
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
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+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml
index fc292cb..2b5878a 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_100to010_G0_10_10.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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                   <rdf:Seq>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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                   <rdf:Bag>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pTet" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
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         </annotation>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:FunctionalComponents>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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@@ -1140,11 +978,8 @@
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-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
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                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
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-                  <cn type="integer"> 1 </cn>
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-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
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+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
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@@ -1182,52 +1014,76 @@
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+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
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@@ -1237,11 +1093,8 @@
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
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+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
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+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
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@@ -1334,11 +1208,8 @@
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-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
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               <apply>
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+                  <times/>
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-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
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-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
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@@ -1376,52 +1244,76 @@
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
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             </apply>
           </math>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
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+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
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-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
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             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1625,11 +1553,8 @@
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
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                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10/Circuit0x8E_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_100to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml
index 0738ba8..4681d31 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0/Circuit0x8E_100to111.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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                   <rdf:Bag>
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+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:FunctionalComponents>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1334,11 +1208,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1431,11 +1323,8 @@
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-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1625,11 +1553,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
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-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml
index 0738ba8..4681d31 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_100to111_G0_10_10.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="300"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="159" layout:y="380"/>
-                      <layout:end layout:x="145" layout:y="320"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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                   <rdf:Bag>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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                   <rdf:Seq>
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+                <mts:Strand>+</mts:Strand>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:ComponentDefinitions>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
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                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1334,11 +1208,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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+              </ModelToSBOL>
             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
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               <rdf:Description rdf:about="#iBioSim10">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
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               <divide/>
@@ -1528,11 +1438,8 @@
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                   <apply>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
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             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1625,11 +1553,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
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-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
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@@ -1722,11 +1668,8 @@
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-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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+                  <times/>
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-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
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+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
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-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10/Circuit0x8E_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_100to111_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1/Circuit0x8E_101to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1/Circuit0x8E_101to000.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1/Circuit0x8E_101to000.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1/Circuit0x8E_101to000.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10/Circuit0x8E_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10/Circuit0x8E_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10/Circuit0x8E_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10/Circuit0x8E_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_101to000_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1/Circuit0x8E_101to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1/Circuit0x8E_101to011.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1/Circuit0x8E_101to011.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1/Circuit0x8E_101to011.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10/Circuit0x8E_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10/Circuit0x8E_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10/Circuit0x8E_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10/Circuit0x8E_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_101to011_G1_10_10_RBA/Circuit0x8E_G1_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml
index 0b82b26..c9deab8 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0/Circuit0x8E_111to010.xml
@@ -1,786 +1,535 @@
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                   <rdf:Bag>
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+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+            </rdf:RDF>
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         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
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-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
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             </apply>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim9">
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1334,11 +1208,8 @@
                   <divide/>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
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+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
               </apply>
             </apply>
           </math>
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-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1625,11 +1553,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
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             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml
index 0b82b26..c9deab8 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_111to010_G0_10_10.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
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+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+            </rdf:RDF>
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         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
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-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
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-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1334,11 +1208,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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                     <mts:Participations>
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1431,11 +1323,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1528,11 +1438,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1625,11 +1553,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1722,11 +1668,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10/Circuit0x8E_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_111to010_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml
index 3d7a277..23704cd 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0/Circuit0x8E_111to100.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="300"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="159" layout:y="380"/>
-                      <layout:end layout:x="145" layout:y="320"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
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                   <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Bag>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                <mts:Strand>+</mts:Strand>
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         </annotation>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                </mts:ComponentDefinitions>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
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+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
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-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
               </apply>
             </apply>
           </math>
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+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1334,11 +1208,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <kineticLaw>
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@@ -1431,11 +1323,8 @@
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-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
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+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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@@ -1528,11 +1438,8 @@
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-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
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                 <plus/>
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-                  <cn type="integer"> 1 </cn>
+                  <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
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+                  <ci> topModel_BetIpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
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-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
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-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
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+        <addedPrefix:kineticLaw>
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@@ -1625,11 +1553,8 @@
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
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+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
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+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
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+        <addedPrefix:listOfProducts>
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+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
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@@ -1722,11 +1668,8 @@
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-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
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+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
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-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
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-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
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+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml
index 3d7a277..23704cd 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_111to100_G0_10_10.xml
@@ -1,786 +1,535 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="300"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="159" layout:y="380"/>
-                      <layout:end layout:x="145" layout:y="320"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="38" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="187" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="126" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="227" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pTet" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim4" id="topModel_HlyIIRpart_module_sub__pTet" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim4">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_HlyIIRpart_module_sub__iBioSim5" id="topModel_HlyIIRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim66" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim67" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim68" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim1" id="topModel_HlyIIRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim14" id="topModel_HlyIIRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim15" id="topModel_HlyIIRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim16" id="topModel_HlyIIRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim17" id="topModel_HlyIIRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim18" id="topModel_HlyIIRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim19" id="topModel_HlyIIRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim20" id="topModel_HlyIIRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim21" id="topModel_HlyIIRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim22" id="topModel_HlyIIRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim23" id="topModel_HlyIIRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim24" id="topModel_HlyIIRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim25" id="topModel_HlyIIRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim26" id="topModel_HlyIIRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_HlyIIRpart_module_sub__iBioSim27" id="topModel_HlyIIRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -788,31 +537,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim73" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim24" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim24">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -820,30 +579,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim75" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim30" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim30">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,30 +620,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim77" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim36" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim36">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +661,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim37" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim37">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +702,40 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim79" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,52 +743,76 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1014,18 +837,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1044,30 +864,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1085,52 +899,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1140,11 +978,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1153,18 +988,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1182,52 +1014,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
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               <divide/>
@@ -1237,11 +1093,8 @@
                   <divide/>
                   <apply>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1250,18 +1103,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1279,52 +1129,76 @@
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+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1334,11 +1208,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1347,18 +1218,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1376,52 +1244,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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+              </ModelToSBOL>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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+                    </mts:Participations>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim8">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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@@ -1431,11 +1323,8 @@
                   <divide/>
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-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1444,18 +1333,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
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-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1473,52 +1359,76 @@
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
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+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim12">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1528,11 +1438,8 @@
                   <divide/>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1541,18 +1448,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1570,52 +1474,76 @@
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             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
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               <rdf:Description rdf:about="#iBioSim7">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1625,11 +1553,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1638,18 +1563,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1667,52 +1589,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
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+                    </mts:Participations>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
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+        <addedPrefix:kineticLaw>
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@@ -1722,11 +1668,8 @@
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-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1735,18 +1678,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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+                  <times/>
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-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
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+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1764,52 +1704,76 @@
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
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+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim9" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1834,18 +1798,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_HlyIIRpart_module_sub__ka </ci>
-                          <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_HlyIIRpart_module_sub__ka </ci>
+                        <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1864,30 +1825,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1905,52 +1860,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_HlyIIRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim12" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_HlyIIRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_HlyIIRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1960,11 +1939,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko </ci>
                     <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
@@ -1973,18 +1949,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
-                      <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_HlyIIRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
+                    <ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_HlyIIRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2002,8 +1975,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10/Circuit0x8E_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_111to100_G0_10_10_RBA/Circuit0x8E_G0_RBA.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1/Circuit0x8E_LHF_000to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1/Circuit0x8E_LHF_000to011.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1/Circuit0x8E_LHF_000to011.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1/Circuit0x8E_LHF_000to011.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1_10_10/Circuit0x8E_LHF_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1_10_10/Circuit0x8E_LHF_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1_10_10/Circuit0x8E_LHF_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to011_G1_10_10/Circuit0x8E_LHF_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1/Circuit0x8E_LHF_000to101.sm.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1/Circuit0x8E_LHF_000to101.sm.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1/Circuit0x8E_LHF_000to101.sm.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1/Circuit0x8E_LHF_000to101.sm.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1_10_10/Circuit0x8E_LHF_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1_10_10/Circuit0x8E_LHF_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1_10_10/Circuit0x8E_LHF_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_000to101_G1_10_10/Circuit0x8E_LHF_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml
index c1e2259..7624a8a 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0/Circuit0x8E_LHF_010to100.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
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         </annotation>
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+      <addedPrefix:species metaid="topModel_AmtRpart_module_sub__iBioSim3" id="topModel_AmtRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
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+            </rdf:RDF>
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         </annotation>
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+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter2_module_sub__iBioSim3" id="topModel_Inverter2_module_sub__Inverter2_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim3">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
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+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pBetI" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim5" id="topModel_YFPpart_module_sub__pBetI" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pPhlF" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim6" id="topModel_YFPpart_module_sub__pPhlF" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter1_module_sub__iBioSim3" id="topModel_Inverter1_module_sub__Inverter1_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim3">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml
index c1e2259..7624a8a 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_010to100_G0_10_10.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="370" layout:y="190"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="16" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
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-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="10"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="840" layout:y="130"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="230" layout:y="140"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="520" layout:y="10"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="261" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="400" layout:y="80"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
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-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="570" layout:y="130"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
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-              <layout:dimensions layout:height="20" layout:width="20"/>
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-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
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-              <layout:dimensions layout:height="20" layout:width="20"/>
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-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to100_G0_10_10/Circuit0x8E_LHF_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml
index 15c5df4..e5e9615 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0/Circuit0x8E_LHF_010to111.xml
@@ -1,848 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="370" layout:y="190"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="16" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="10"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="840" layout:y="130"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="230" layout:y="140"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="520" layout:y="10"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="261" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="400" layout:y="80"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="570" layout:y="130"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="420" layout:y="100"/>
-                      <layout:end layout:x="580" layout:y="140"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="125" layout:y="370"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="135" layout:y="290"/>
-                      <layout:end layout:x="135" layout:y="380"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="90"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__YFP_degradation_interaction__substrate__YFP_protein" layout:role="substrate" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="70" layout:y="100"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="380" layout:y="260"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
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                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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                   <rdf:Seq>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+      </addedPrefix:species>
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                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
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                   <rdf:Seq>
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+                <mts:Strand>+</mts:Strand>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -850,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
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-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
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+                    </mts:Participations>
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-                    </speciesReference>
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-        <kineticLaw>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
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             <apply>
               <times/>
@@ -944,30 +697,40 @@
               <ci> YFP_protein </ci>
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           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -975,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1006,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1061,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1074,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1103,52 +894,76 @@
               </apply>
             </apply>
           </math>
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-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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@@ -1158,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1171,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1200,52 +1009,76 @@
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-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1270,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1300,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1341,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1396,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1409,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1438,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1493,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1506,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1535,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1590,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1603,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1632,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1687,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1700,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1729,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1799,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1829,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1870,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1925,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1938,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1967,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2022,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2035,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2064,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2095,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml
index 15c5df4..e5e9615 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_010to111_G0_10_10.xml
@@ -1,848 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
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         </annotation>
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+      <addedPrefix:species metaid="topModel_AmtRpart_module_sub__iBioSim3" id="topModel_AmtRpart_module_sub__pBAD" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
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+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter2_module_sub__iBioSim3" id="topModel_Inverter2_module_sub__Inverter2_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
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+                <mts:DNAComponents>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pBetI" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim5" id="topModel_YFPpart_module_sub__pBetI" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pPhlF" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim6" id="topModel_YFPpart_module_sub__pPhlF" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim6">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter1_module_sub__iBioSim3" id="topModel_Inverter1_module_sub__Inverter1_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim3">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -850,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -882,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -913,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -944,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -975,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1006,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1061,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1074,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1103,52 +894,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1158,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1171,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1200,52 +1009,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1270,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1300,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1341,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1396,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1409,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1438,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1493,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1506,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1535,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1590,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1603,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1632,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1687,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1700,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1729,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1799,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1829,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1870,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1925,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1938,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1967,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2022,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2035,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2064,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2095,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_010to111_G0_10_10/Circuit0x8E_LHF_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1/Circuit0x8E_LHF_011to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1/Circuit0x8E_LHF_011to000.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1/Circuit0x8E_LHF_011to000.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1/Circuit0x8E_LHF_011to000.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1_10_10/Circuit0x8E_LHF_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1_10_10/Circuit0x8E_LHF_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1_10_10/Circuit0x8E_LHF_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to000_G1_10_10/Circuit0x8E_LHF_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1/Circuit0x8E_LHF_011to101.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1/Circuit0x8E_LHF_011to101.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1/Circuit0x8E_LHF_011to101.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1/Circuit0x8E_LHF_011to101.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1_10_10/Circuit0x8E_LHF_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1_10_10/Circuit0x8E_LHF_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1_10_10/Circuit0x8E_LHF_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_011to101_G1_10_10/Circuit0x8E_LHF_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml
index b1e2fea..5176ef2 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0/Circuit0x8E_LHF_100to010.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="370" layout:y="190"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="16" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="10"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="840" layout:y="130"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="230" layout:y="140"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="520" layout:y="10"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="261" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="400" layout:y="80"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="570" layout:y="130"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="420" layout:y="100"/>
-                      <layout:end layout:x="580" layout:y="140"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="125" layout:y="370"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="135" layout:y="290"/>
-                      <layout:end layout:x="135" layout:y="380"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="90"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__YFP_degradation_interaction__substrate__YFP_protein" layout:role="substrate" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="70" layout:y="100"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="380" layout:y="260"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="390" layout:y="210"/>
-                      <layout:end layout:x="390" layout:y="270"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BetI_degradation_interaction" layout:reaction="BetI_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="860" layout:y="220"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BetI_degradation_interaction__substrate__BetI_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BetI_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="860" layout:y="150"/>
-                      <layout:end layout:x="870" layout:y="230"/>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
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-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="276" layout:y="280"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="250" layout:y="160"/>
-                      <layout:end layout:x="286" layout:y="290"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="860" layout:y="150"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
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-                  <layout:listOfCurveSegments>
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-                      <layout:start layout:x="390" layout:y="210"/>
-                      <layout:end layout:x="860" layout:y="150"/>
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-              </layout:speciesReferenceGlyph>
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-          <layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__BetI_protein">
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-              <layout:position layout:x="860" layout:y="150"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
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-                      <layout:end layout:x="860" layout:y="150"/>
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-              </layout:speciesReferenceGlyph>
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-              <layout:position layout:x="250" layout:y="160"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
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-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="150" layout:y="25"/>
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-                    </layout:curveSegment>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_protein__repression__AmtR_protein">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
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-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim39">
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                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
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@@ -1007,52 +779,76 @@
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-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
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                   <rdf:Description rdf:about="#iBioSim8">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
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@@ -1062,11 +858,8 @@
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                   <apply>
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-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
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+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
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             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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@@ -1159,11 +973,8 @@
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-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
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                 <apply>
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+                  <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
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+                  <ci> topModel_BetIpart_module_sub__nr </ci>
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                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
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+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_100to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_100to010_G0_10_10.xml
index b1e2fea..5176ef2 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_100to010_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_100to010_G0_10_10.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="370" layout:y="190"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="16" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="10"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="840" layout:y="130"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="230" layout:y="140"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="520" layout:y="10"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="261" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="400" layout:y="80"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="570" layout:y="130"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pBetI" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim5" id="topModel_YFPpart_module_sub__pBetI" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
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+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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         </annotation>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pPhlF" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim6" id="topModel_YFPpart_module_sub__pPhlF" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter1_module_sub__iBioSim3" id="topModel_Inverter1_module_sub__Inverter1_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim3">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
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             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
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           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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+          </ModelToSBOL>
         </annotation>
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-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
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           </math>
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-      </reaction>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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                   <rdf:Description rdf:about="#">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-                    </modifierSpeciesReference>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
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+        </addedPrefix:kineticLaw>
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+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
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+        <addedPrefix:listOfProducts>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
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+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
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diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to010_G0_10_10/Circuit0x8E_LHF_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0/Circuit0x8E_LHF_100to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0/Circuit0x8E_LHF_100to111.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0/Circuit0x8E_LHF_100to111.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0/Circuit0x8E_LHF_100to111.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml
index d9f22e7..d77b8ff 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_100to111_G0_10_10.xml
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+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim12">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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+                </rdf:RDF>
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-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
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-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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@@ -1591,11 +1472,8 @@
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                   <apply>
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-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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         </annotation>
-              <listOfProducts>
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+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
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             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_100to111_G0_10_10/Circuit0x8E_LHF_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1/Circuit0x8E_LHF_101to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1/Circuit0x8E_LHF_101to000.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1/Circuit0x8E_LHF_101to000.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1/Circuit0x8E_LHF_101to000.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1_10_10/Circuit0x8E_LHF_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1_10_10/Circuit0x8E_LHF_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1_10_10/Circuit0x8E_LHF_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to000_G1_10_10/Circuit0x8E_LHF_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1/Circuit0x8E_LHF_101to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1/Circuit0x8E_LHF_101to011.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1/Circuit0x8E_LHF_101to011.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1/Circuit0x8E_LHF_101to011.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1_10_10/Circuit0x8E_LHF_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1_10_10/Circuit0x8E_LHF_G1.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1_10_10/Circuit0x8E_LHF_G1.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_101to011_G1_10_10/Circuit0x8E_LHF_G1.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml
index c3dd077..4e93765 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0/Circuit0x8E_LHF_111to010.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="370" layout:y="190"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="16" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="10"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="840" layout:y="130"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="230" layout:y="140"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="520" layout:y="10"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="261" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="400" layout:y="80"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="570" layout:y="130"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="420" layout:y="100"/>
-                      <layout:end layout:x="580" layout:y="140"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="125" layout:y="370"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="135" layout:y="290"/>
-                      <layout:end layout:x="135" layout:y="380"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="90"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__YFP_degradation_interaction__substrate__YFP_protein" layout:role="substrate" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="70" layout:y="100"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="380" layout:y="260"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="390" layout:y="210"/>
-                      <layout:end layout:x="390" layout:y="270"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
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-              </layout:speciesReferenceGlyph>
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                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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+                </mts:ComponentDefinitions>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
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+            </rdf:RDF>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter1_module_sub__iBioSim3" id="topModel_Inverter1_module_sub__Inverter1_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim3">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
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+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
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+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
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+            </rdf:RDF>
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         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
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-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
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-        <kineticLaw>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#">
                 <mts:Interactions>
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
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               <rdf:Description rdf:about="#iBioSim7">
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                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
               </apply>
             </apply>
           </math>
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-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
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-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml
index c3dd077..4e93765 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_111to010_G0_10_10.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
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         </annotation>
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+      <addedPrefix:species metaid="topModel_Inverter2_module_sub__iBioSim3" id="topModel_Inverter2_module_sub__Inverter2_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pBetI" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim5" id="topModel_YFPpart_module_sub__pBetI" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
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+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pPhlF" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim6" id="topModel_YFPpart_module_sub__pPhlF" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter1_module_sub__iBioSim3" id="topModel_Inverter1_module_sub__Inverter1_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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               <rdf:Description rdf:about="#iBioSim3">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
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                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
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+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
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+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
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             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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+                </rdf:RDF>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
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+                  </rdf:Description>
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             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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         </annotation>
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-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
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+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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               <divide/>
@@ -1397,11 +1244,8 @@
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                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
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                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
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                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
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+                </rdf:RDF>
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             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim11">
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                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to010_G0_10_10/Circuit0x8E_LHF_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml
index e1e4c89..229429f 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0/Circuit0x8E_LHF_111to100.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="370" layout:y="190"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="16" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="10"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="840" layout:y="130"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="230" layout:y="140"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="520" layout:y="10"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="261" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="400" layout:y="80"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="570" layout:y="130"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="420" layout:y="100"/>
-                      <layout:end layout:x="580" layout:y="140"/>
-                    </layout:curveSegment>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="125" layout:y="370"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
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-                      <layout:end layout:x="135" layout:y="380"/>
-                    </layout:curveSegment>
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-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="90"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
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-                      <layout:end layout:x="70" layout:y="100"/>
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-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="380" layout:y="260"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
-                <layout:curve>
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-                      <layout:end layout:x="390" layout:y="270"/>
-                    </layout:curveSegment>
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-              </layout:speciesReferenceGlyph>
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-            <layout:boundingBox>
-              <layout:position layout:x="860" layout:y="220"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BetI_degradation_interaction__substrate__BetI_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BetI_protein">
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
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+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
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+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
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                   <rdf:Description rdf:about="#iBioSim9">
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                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
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         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
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                     <mts:Participations>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
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                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
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             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
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+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
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               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
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+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
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+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
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+                    </mts:Participations>
+                  </rdf:Description>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
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             </annotation>
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-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
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                   <rdf:Description rdf:about="#iBioSim8">
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
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+                  </rdf:Description>
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             </annotation>
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-        <kineticLaw>
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+        <addedPrefix:kineticLaw>
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             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
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                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml
index e1e4c89..229429f 100644
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml
+++ b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_111to100_G0_10_10.xml
@@ -1,849 +1,571 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim3" id="topModel" name="Created by iBioSim flatten routine">
     <annotation>
       <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
         <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
           <rdf:Description rdf:about="#iBioSim1">
             <mts:ModuleDefinitions>
               <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
+                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/>
+              </rdf:Bag>
+            </mts:ModuleDefinitions>
+          </rdf:Description>
+        </rdf:RDF>
+      </ModelToSBOL>
     </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="50"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="45" layout:y="70"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="370" layout:y="190"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="16" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="10"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="840" layout:y="130"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="230" layout:y="140"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="520" layout:y="10"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="261" layout:y="360"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="400" layout:y="80"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="570" layout:y="130"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="420" layout:y="100"/>
-                      <layout:end layout:x="580" layout:y="140"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="125" layout:y="370"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="135" layout:y="290"/>
-                      <layout:end layout:x="135" layout:y="380"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="90"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__YFP_degradation_interaction__substrate__YFP_protein" layout:role="substrate" layout:speciesGlyph="Glyph__YFP_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="281" layout:y="380"/>
-                      <layout:end layout:x="70" layout:y="100"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="380" layout:y="260"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_YFPpart_module_sub__pPhlF" initialAmount="2" metaid="topModel_YFPpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_YFPpart_module_sub__iBioSim6" id="topModel_YFPpart_module_sub__pPhlF" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim3" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_Inverter1_module_sub__iBioSim3" id="topModel_Inverter1_module_sub__Inverter1_fc" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim3">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim5" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim5" id="topModel_PhlFpart_module_sub__pTac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" sboTerm="SBO:0000590">
+      </addedPrefix:species>
+      <addedPrefix:species metaid="topModel_PhlFpart_module_sub__iBioSim6" id="topModel_PhlFpart_module_sub__pAmtR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim6">
                 <mts:ComponentDefinitions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:ComponentDefinitions>
+                <mts:FunctionalComponents>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Bag>
+                </mts:FunctionalComponents>
+                <mts:DNAComponents>
                   <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/>
+                  </rdf:Seq>
+                </mts:DNAComponents>
+                <mts:Strand>+</mts:Strand>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim70" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim71" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim72" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:species>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim1" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim70" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim71" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim72" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim1" id="topModel_BetIpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim14" id="topModel_BetIpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim15" id="topModel_BetIpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim16" id="topModel_BetIpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim17" id="topModel_BetIpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim18" id="topModel_BetIpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim19" id="topModel_BetIpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim20" id="topModel_BetIpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim21" id="topModel_BetIpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim22" id="topModel_BetIpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim23" id="topModel_BetIpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim24" id="topModel_BetIpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim25" id="topModel_BetIpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim26" id="topModel_BetIpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_BetIpart_module_sub__iBioSim27" id="topModel_BetIpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim1" id="topModel_AmtRpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim14" id="topModel_AmtRpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim15" id="topModel_AmtRpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim16" id="topModel_AmtRpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim17" id="topModel_AmtRpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim18" id="topModel_AmtRpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim19" id="topModel_AmtRpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim20" id="topModel_AmtRpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim21" id="topModel_AmtRpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim22" id="topModel_AmtRpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim23" id="topModel_AmtRpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim24" id="topModel_AmtRpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim25" id="topModel_AmtRpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim26" id="topModel_AmtRpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_AmtRpart_module_sub__iBioSim27" id="topModel_AmtRpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim1" id="topModel_Inverter2_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim9" id="topModel_Inverter2_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim10" id="topModel_Inverter2_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim11" id="topModel_Inverter2_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim12" id="topModel_Inverter2_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim13" id="topModel_Inverter2_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim14" id="topModel_Inverter2_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim15" id="topModel_Inverter2_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim16" id="topModel_Inverter2_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim17" id="topModel_Inverter2_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim18" id="topModel_Inverter2_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim19" id="topModel_Inverter2_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim20" id="topModel_Inverter2_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim21" id="topModel_Inverter2_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter2_module_sub__iBioSim22" id="topModel_Inverter2_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim1" id="topModel_YFPpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim14" id="topModel_YFPpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim15" id="topModel_YFPpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim16" id="topModel_YFPpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim17" id="topModel_YFPpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim18" id="topModel_YFPpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim19" id="topModel_YFPpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim20" id="topModel_YFPpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim21" id="topModel_YFPpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim22" id="topModel_YFPpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim23" id="topModel_YFPpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim24" id="topModel_YFPpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim25" id="topModel_YFPpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim26" id="topModel_YFPpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_YFPpart_module_sub__iBioSim27" id="topModel_YFPpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim1" id="topModel_Inverter1_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim9" id="topModel_Inverter1_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim10" id="topModel_Inverter1_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim11" id="topModel_Inverter1_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim12" id="topModel_Inverter1_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim13" id="topModel_Inverter1_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim14" id="topModel_Inverter1_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim15" id="topModel_Inverter1_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim16" id="topModel_Inverter1_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim17" id="topModel_Inverter1_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim18" id="topModel_Inverter1_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim19" id="topModel_Inverter1_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim20" id="topModel_Inverter1_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim21" id="topModel_Inverter1_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_Inverter1_module_sub__iBioSim22" id="topModel_Inverter1_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim1" id="topModel_PhlFpart_module_sub__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim14" id="topModel_PhlFpart_module_sub__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim15" id="topModel_PhlFpart_module_sub__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim16" id="topModel_PhlFpart_module_sub__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim17" id="topModel_PhlFpart_module_sub__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim18" id="topModel_PhlFpart_module_sub__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim19" id="topModel_PhlFpart_module_sub__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim20" id="topModel_PhlFpart_module_sub__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim21" id="topModel_PhlFpart_module_sub__nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim22" id="topModel_PhlFpart_module_sub__nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim23" id="topModel_PhlFpart_module_sub__ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim24" id="topModel_PhlFpart_module_sub__kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim25" id="topModel_PhlFpart_module_sub__ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim26" id="topModel_PhlFpart_module_sub__np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="topModel_PhlFpart_module_sub__iBioSim27" id="topModel_PhlFpart_module_sub__ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <lt/>
@@ -851,31 +573,41 @@
             <cn type="integer"> 30 </cn>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim77" reversible="false">
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim77" id="BM3R1_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim25" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim25">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -883,30 +615,40 @@
               <ci> BM3R1_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim78" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim78" id="PhlF_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim26" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim26">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -914,30 +656,40 @@
               <ci> PhlF_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim80" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim80" id="YFP_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim32" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim32">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -945,30 +697,40 @@
               <ci> YFP_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim82" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim82" id="HlyIIR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim38" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim38">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -976,30 +738,40 @@
               <ci> HlyIIR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim83" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim83" id="BetI_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim39" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim39">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1007,52 +779,76 @@
               <ci> BetI_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1062,11 +858,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pTet </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1075,18 +868,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1104,52 +894,76 @@
               </apply>
             </apply>
           </math>
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-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_BetIpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" reversible="false">
         <annotation>
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               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
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-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
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+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1159,11 +973,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
+                    <ci> topModel_BetIpart_module_sub__ko </ci>
                     <ci> topModel_BetIpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_BetIpart_module_sub__ko_r </ci>
@@ -1172,18 +983,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
+                    <ci> topModel_BetIpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_BetIpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1201,52 +1009,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBM3R1">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1271,18 +1103,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_AmtRpart_module_sub__ka </ci>
-                          <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_AmtRpart_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_AmtRpart_module_sub__ka </ci>
+                        <ci> topModel_AmtRpart_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_AmtRpart_module_sub__nr </ci>
+                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_AmtRpart_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1301,30 +1130,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__kao_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__kao_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1342,52 +1165,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_AmtRpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pBAD">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein_pBM3R1_repression/AmtRpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BM3R1_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1397,11 +1244,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_AmtRpart_module_sub__pBAD </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_AmtRpart_module_sub__pBAD </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko </ci>
                     <ci> topModel_AmtRpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_AmtRpart_module_sub__ko_r </ci>
@@ -1410,18 +1254,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_AmtRpart_module_sub__ko_f </ci>
-                      <ci> topModel_AmtRpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_AmtRpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_AmtRpart_module_sub__ko_f </ci>
+                    <ci> topModel_AmtRpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_AmtRpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1439,52 +1280,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" metaid="topModel_Inverter2_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter2_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter2_module_sub__BM3R1_protein_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter2_module_sub___iBioSim7" species="BM3R1_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter2_module_sub__Inverter2_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/BM3R1_protein_interaction/Inverter2_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein_pTet_repression/Inverter2_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter2_module_sub___iBioSim6" sboTerm="SBO:0000020" species="TetR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter2_module/TetR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1494,11 +1357,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
-                      <ci> topModel_Inverter2_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_Inverter2_module_sub__Inverter2_fc </ci>
+                    <ci> topModel_Inverter2_module_sub__ko </ci>
                     <ci> topModel_Inverter2_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_Inverter2_module_sub__ko_r </ci>
@@ -1507,18 +1367,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter2_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter2_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter2_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter2_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter2_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter2_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1536,52 +1393,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim9" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pBetI">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1591,11 +1472,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pBetI </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pBetI </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1604,18 +1482,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1633,52 +1508,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_YFPpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_YFPpart_module_sub___iBioSim12" species="YFP_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_YFPpart_module_sub__pPhlF">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_YFPpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1688,11 +1587,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_YFPpart_module_sub__pPhlF </ci>
-                      <ci> topModel_YFPpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_YFPpart_module_sub__pPhlF </ci>
+                    <ci> topModel_YFPpart_module_sub__ko </ci>
                     <ci> topModel_YFPpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_YFPpart_module_sub__ko_r </ci>
@@ -1701,18 +1597,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_YFPpart_module_sub__ko_f </ci>
-                      <ci> topModel_YFPpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_YFPpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_YFPpart_module_sub__ko_f </ci>
+                    <ci> topModel_YFPpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_YFPpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1730,52 +1623,74 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" metaid="topModel_Inverter1_module_sub__iBioSim5" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_Inverter1_module_sub__iBioSim5" sboTerm="SBO:0000589" id="topModel_Inverter1_module_sub__HlyIIR_protein_interaction" reversible="false">
         <annotation>
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             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim5">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_Inverter1_module_sub___iBioSim7" species="HlyIIR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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                   <rdf:Description rdf:about="#iBioSim7">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_Inverter1_module_sub__Inverter1_fc">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/HlyIIR_protein_interaction/Inverter1_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein_pBAD_activation/Inverter1_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_Inverter1_module_sub___iBioSim6" sboTerm="SBO:0000459" species="Ara_AraC_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim6">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/Ara_AraC_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1800,18 +1715,15 @@
                   <apply>
                     <times/>
                     <apply>
-                      <times/>
+                      <divide/>
                       <apply>
-                        <divide/>
-                        <apply>
-                          <times/>
-                          <ci> topModel_Inverter1_module_sub__ka </ci>
-                          <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                        </apply>
-                        <ci> topModel_Inverter1_module_sub__kao_r </ci>
+                        <times/>
+                        <ci> topModel_Inverter1_module_sub__ka </ci>
+                        <ci> topModel_Inverter1_module_sub__kao_f </ci>
                       </apply>
-                      <ci> topModel_Inverter1_module_sub__nr </ci>
+                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
                     </apply>
+                    <ci> topModel_Inverter1_module_sub__nr </ci>
                     <apply>
                       <power/>
                       <apply>
@@ -1830,30 +1742,24 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
+                    <ci> topModel_Inverter1_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kao_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kao_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_Inverter1_module_sub__kao_f </ci>
+                    <ci> topModel_Inverter1_module_sub__kao_r </ci>
                   </apply>
+                  <ci> topModel_Inverter1_module_sub__nr </ci>
                   <apply>
                     <power/>
                     <apply>
@@ -1871,52 +1777,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim7" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim7">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim9">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim8">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1926,11 +1856,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pTac </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pTac </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -1939,18 +1866,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1968,52 +1892,76 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="topModel_PhlFpart_module_sub__iBioSim10" sboTerm="SBO:0000589" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#iBioSim10">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim12">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
+          </addedPrefix:modifierSpeciesReference>
+          <addedPrefix:modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_protein">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim11">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein/1"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
+          </addedPrefix:modifierSpeciesReference>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -2023,11 +1971,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko </ci>
-                    </apply>
+                    <ci> topModel_PhlFpart_module_sub__pAmtR </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko </ci>
                     <ci> topModel_PhlFpart_module_sub__ko_f </ci>
                   </apply>
                   <ci> topModel_PhlFpart_module_sub__ko_r </ci>
@@ -2036,18 +1981,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_PhlFpart_module_sub__ko_f </ci>
-                      <ci> topModel_PhlFpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_PhlFpart_module_sub__nr </ci>
+                    <divide/>
+                    <ci> topModel_PhlFpart_module_sub__ko_f </ci>
+                    <ci> topModel_PhlFpart_module_sub__ko_r </ci>
                   </apply>
+                  <ci> topModel_PhlFpart_module_sub__nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -2065,30 +2007,40 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim84" reversible="false">
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim84" id="AmtR_degradation_interaction" reversible="false">
         <annotation>
           <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
             <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
               <rdf:Description rdf:about="#">
                 <mts:Interactions>
                   <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
+                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/>
+                  </rdf:Bag>
+                </mts:Interactions>
+              </rdf:Description>
+            </rdf:RDF>
+          </ModelToSBOL>
         </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference metaid="iBioSim40" species="AmtR_protein" stoichiometry="10">
             <annotation>
               <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
                 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
                   <rdf:Description rdf:about="#iBioSim40">
                     <mts:Participations>
                       <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
+                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/>
+                      </rdf:Bag>
+                    </mts:Participations>
+                  </rdf:Description>
+                </rdf:RDF>
+              </ModelToSBOL>
             </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
+          </addedPrefix:speciesReference>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -2096,8 +2048,8 @@
               <ci> AmtR_protein </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_G0.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_G0.props
similarity index 100%
rename from GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_G0.csl
rename to GeneticCircuits/Circuit0x8E/Circuit0x8E_LHF_111to100_G0_10_10/Circuit0x8E_LHF_G0.props
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.sm
deleted file mode 100644
index b8b47f0..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml
deleted file mode 100644
index b91be7e..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
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-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
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-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
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-                    <ci> LacI_protein </ci>
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-              </apply>
-            </apply>
-          </math>
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-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
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-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
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-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
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-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
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-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
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-                  <plus/>
-                  <cn type="integer"> 1 </cn>
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-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
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-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
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-                <apply>
-                  <power/>
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-                    <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
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-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
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-              <ci> AmtR_protein </ci>
-            </apply>
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-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
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diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011_bound.sm
deleted file mode 100644
index 35f11c3..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1/Circuit0x8E_TI_000to011_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_000to011.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.sm
deleted file mode 100644
index b327658..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml
deleted file mode 100644
index b91be7e..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
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-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
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-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
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-            </layout:listOfSpeciesReferenceGlyphs>
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-          <layout:reactionGlyph layout:id="Glyph__SrpR_degradation_interaction" layout:reaction="SrpR_degradation_interaction">
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-              <layout:position layout:x="600" layout:y="230"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_degradation_interaction" layout:reaction="TetR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="890" layout:y="20"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="560" layout:y="80"/>
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-                      <layout:end layout:x="570" layout:y="90"/>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim3" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim3">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim4">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
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-            </annotation>
-                    </speciesReference>
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-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim8">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10_bound.sm
deleted file mode 100644
index 35f11c3..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_000to011_G1_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_000to011.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_G1.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to011_G1_10_10/Circuit0x8E_TI_G1.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.sm
deleted file mode 100644
index 1c01cde..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml
deleted file mode 100644
index cffad67..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
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-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
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-            </layout:listOfSpeciesReferenceGlyphs>
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-          <layout:reactionGlyph layout:id="Glyph__TetR_degradation_interaction" layout:reaction="TetR_degradation_interaction">
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-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
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-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
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-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="338" layout:y="110"/>
-                      <layout:end layout:x="300" layout:y="210"/>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BetI_degradation_interaction" layout:reaction="BetI_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="940" layout:y="200"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
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-    <listOfParameters>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
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-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
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-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
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-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
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-            <annotation>
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-                  <rdf:Description rdf:about="#iBioSim23">
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-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
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-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
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-              <listOfReactants>
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-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
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-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
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-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101_bound.sm
deleted file mode 100644
index 4562659..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1/Circuit0x8E_TI_000to101_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_000to101.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.sm
deleted file mode 100644
index af52709..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml
deleted file mode 100644
index cffad67..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-    <listOfParameters>
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-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
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-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
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-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
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-        <annotation>
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-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
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-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
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-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
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-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
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-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim28">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
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-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim87" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim34">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="LacI_degradation_interaction" metaid="iBioSim88" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim35" species="LacI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim35">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
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-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim89" reversible="false">
-        <annotation>
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-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
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-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim40">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> HlyIIR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
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-        <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10_bound.sm
deleted file mode 100644
index 4562659..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_000to101_G1_10_10/Circuit0x8E_TI_000to101_G1_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_000to101.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.sm
deleted file mode 100644
index ce8174b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml
deleted file mode 100644
index 151ce56..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
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-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
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-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
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-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
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-        </math>
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-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
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-          </math>
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-        <annotation>
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-        </annotation>
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-            <annotation>
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-              <ci> kd </ci>
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-                    <ci> LacI_protein </ci>
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-                  </apply>
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-                <apply>
-                  <power/>
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-                    <times/>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
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-                  <ci> topModel_BetIpart_module_sub__nc </ci>
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-              </apply>
-            </apply>
-          </math>
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-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
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-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
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-                <ci> topModel_BetIpart_module_sub__nr </ci>
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-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
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-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
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-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
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-            </apply>
-          </math>
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-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
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-              <ci> Ara_AraC_protein </ci>
-            </apply>
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diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000_bound.sm
deleted file mode 100644
index dc5baca..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to000_G1/Circuit0x8E_TI_011to000_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_011to000.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.sm
deleted file mode 100644
index 892e1f6..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 70;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 0;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml
deleted file mode 100644
index 52e2152..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100.xml
+++ /dev/null
@@ -1,2619 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="360"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="250"/>
-                      <layout:end layout:x="90" layout:y="370"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__SrpR_degradation_interaction" layout:reaction="SrpR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="600" layout:y="230"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__SrpR_degradation_interaction__substrate__SrpR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__SrpR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="458" layout:y="200"/>
-                      <layout:end layout:x="610" layout:y="240"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_degradation_interaction" layout:reaction="TetR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="890" layout:y="20"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim5">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
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-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim4" sboTerm="SBO:0000590">
-        <annotation>
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-              <rdf:Description rdf:about="#iBioSim4">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
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-                  <rdf:Bag>
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-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim3" sboTerm="SBO:0000590">
-        <annotation>
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-              <rdf:Description rdf:about="#iBioSim3">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim4">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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-        </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
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-                      <ci> topModel_Inverter1_module_sub__kr_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> LacI_protein </ci>
-                  </apply>
-                  <ci> topModel_Inverter1_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim7">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim9">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim8">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100_bound.sm
deleted file mode 100644
index ec11386..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0/Circuit0x8E_TI_010to100_bound.sm
+++ /dev/null
@@ -1,442 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_010to100.xml
-
-// EXPECTED PROBABILITY: 47.307%
-// STAMINA PROBABILITY: 0.9999999999998181 - 1.0
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.sm
deleted file mode 100644
index dfa1a4a..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 70;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 0;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml
deleted file mode 100644
index 52e2152..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10.xml
+++ /dev/null
@@ -1,2619 +0,0 @@
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-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
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-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
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-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
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-              <rdf:Description rdf:about="#">
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-              <ci> SrpR_protein </ci>
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-        <annotation>
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-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
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-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
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-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10_bound.sm
deleted file mode 100644
index ec11386..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_010to100_G0_10_10_bound.sm
+++ /dev/null
@@ -1,442 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_010to100.xml
-
-// EXPECTED PROBABILITY: 47.307%
-// STAMINA PROBABILITY: 0.9999999999998181 - 1.0
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_G0csl.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to100_G0_10_10/Circuit0x8E_TI_G0csl.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.sm
deleted file mode 100644
index 35b03dd..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml
deleted file mode 100644
index 815e0b1..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-    <listOfParameters>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="TetR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim28">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim87" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim34">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="LacI_degradation_interaction" metaid="iBioSim88" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim35" species="LacI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim35">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
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-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101_bound.sm
deleted file mode 100644
index c13ad84..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to101_G1/Circuit0x8E_TI_011to101_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_011to101.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.sm
deleted file mode 100644
index 0910313..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 70;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 0;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml
deleted file mode 100644
index f0d89a2..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
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-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
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-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
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-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
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-        </annotation>
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
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-      </reaction>
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-        <annotation>
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-              <rdf:Description rdf:about="#">
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-        </annotation>
-              <listOfReactants>
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-            <annotation>
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-                      <rdf:Bag>
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-            </annotation>
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim87" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
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-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim34">
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-            </annotation>
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <times/>
-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
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-          </math>
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-        <annotation>
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-        </annotation>
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-              <ci> kd </ci>
-              <ci> LacI_protein </ci>
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-        </annotation>
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-        </annotation>
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diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111_bound.sm
deleted file mode 100644
index 2bd631c..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0/Circuit0x8E_TI_010to111_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_010to111.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.sm
deleted file mode 100644
index 66ebd53..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 70;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 0;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml
deleted file mode 100644
index f0d89a2..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="360"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="250"/>
-                      <layout:end layout:x="90" layout:y="370"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__SrpR_degradation_interaction" layout:reaction="SrpR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="600" layout:y="230"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__SrpR_degradation_interaction__substrate__SrpR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__SrpR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="458" layout:y="200"/>
-                      <layout:end layout:x="610" layout:y="240"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_degradation_interaction" layout:reaction="TetR_degradation_interaction">
-            <layout:boundingBox>
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-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim5">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_Inverter1_module_sub__Inverter1_fc" initialAmount="2" metaid="topModel_Inverter1_module_sub__iBioSim4" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim4">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim3" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim3">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim4">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
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-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kr_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> LacI_protein </ci>
-                  </apply>
-                  <ci> topModel_Inverter1_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim7">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
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-              <listOfProducts>
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-                    </speciesReference>
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-        <listOfModifiers>
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-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
-            <annotation>
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-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10_bound.sm
deleted file mode 100644
index 2bd631c..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_010to111_G0_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_010to111.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 70; // Initial amount 70
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 0; // Initial amount 0
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_G0csl.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_010to111_G0_10_10/Circuit0x8E_TI_G0csl.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.sm
deleted file mode 100644
index af120b9..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml
deleted file mode 100644
index 151ce56..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
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-                  </layout:listOfCurveSegments>
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-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
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-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
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-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
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-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
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-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
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-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
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-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
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-              <layout:dimensions layout:height="40" layout:width="40"/>
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-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
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-              <layout:dimensions layout:height="40" layout:width="40"/>
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-        <layout:listOfReactionGlyphs>
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-    <listOfParameters>
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-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="TetR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
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-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10_bound.sm
deleted file mode 100644
index dc5baca..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_011to000_G1_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_011to000.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_G1.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to000_G1_10_10/Circuit0x8E_TI_G1.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.sm
deleted file mode 100644
index f438e87..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 0;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 70;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 0;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml
deleted file mode 100644
index 815e0b1..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
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-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
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-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
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-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
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-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
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-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
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-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
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-    <listOfParameters>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
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-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
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-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="TetR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim28">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10_bound.sm
deleted file mode 100644
index c13ad84..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_011to101_G1_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_011to101.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 0; // Initial amount 0
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 70; // Initial amount 70
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 0; // Initial amount 0
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_G1.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_G1.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_011to101_G1_10_10/Circuit0x8E_TI_G1.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.sm
deleted file mode 100644
index 6b14d82..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml
deleted file mode 100644
index 59d639c..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-    <listOfParameters>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
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-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
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-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
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-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
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-        </annotation>
-              <listOfReactants>
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-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim28">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim87" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim34">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="LacI_degradation_interaction" metaid="iBioSim88" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim35" species="LacI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim35">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim89" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
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-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010_bound.sm
deleted file mode 100644
index 3175604..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0/Circuit0x8E_TI_100to010_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_100to010.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.sm
deleted file mode 100644
index 9faa1ac..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml
deleted file mode 100644
index 59d639c..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
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-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
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-        </math>
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-    </listOfConstraints>
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-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
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-      </reaction>
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-        <annotation>
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-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
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-        <annotation>
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-              <ci> LacI_protein </ci>
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diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10_bound.sm
deleted file mode 100644
index 3175604..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_100to010_G0_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_100to010.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_G0csl.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to010_G0_10_10/Circuit0x8E_TI_G0csl.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.sm
deleted file mode 100644
index a83e9bd..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml
deleted file mode 100644
index b8d47e7..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="360"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="250"/>
-                      <layout:end layout:x="90" layout:y="370"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
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-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
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-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter1_module_sub__Inverter1_fc </ci>
-                      <ci> topModel_Inverter1_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_Inverter1_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kr_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> LacI_protein </ci>
-                  </apply>
-                  <ci> topModel_Inverter1_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim7">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
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-            <annotation>
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-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111_bound.sm
deleted file mode 100644
index 099bf23..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0/Circuit0x8E_TI_100to111_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_100to111.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.sm
deleted file mode 100644
index 9a52d2b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 0;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 70;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml
deleted file mode 100644
index b8d47e7..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="360"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
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-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="250"/>
-                      <layout:end layout:x="90" layout:y="370"/>
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-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__SrpR_degradation_interaction" layout:reaction="SrpR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="600" layout:y="230"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__SrpR_degradation_interaction__substrate__SrpR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__SrpR_protein">
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-                  <layout:listOfCurveSegments>
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-                      <layout:start layout:x="458" layout:y="200"/>
-                      <layout:end layout:x="610" layout:y="240"/>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_degradation_interaction" layout:reaction="TetR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="890" layout:y="20"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__TetR_degradation_interaction__substrate__TetR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__TetR_protein">
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-                      <layout:end layout:x="900" layout:y="30"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="560" layout:y="80"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
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-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
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-                      <layout:end layout:x="570" layout:y="90"/>
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-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
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-              <layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim3" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim3">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim4">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
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-            </annotation>
-                    </speciesReference>
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-        <listOfModifiers>
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-            <annotation>
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-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
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-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim8">
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-                      <rdf:Bag>
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-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10_bound.sm
deleted file mode 100644
index 099bf23..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_100to111_G0_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_100to111.xml
-
-ctmc
-
-const int MAX_AMOUNT = 100;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0; // Initial amount 0
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 70; // Initial amount 70
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_G0csl.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_100to111_G0_10_10/Circuit0x8E_TI_G0csl.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.sm
deleted file mode 100644
index 89f5e4b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 250;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 0;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml
deleted file mode 100644
index 2e9f85f..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
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-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="360"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-                    <layout:curveSegment xsi:type="LineSegment">
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-                      <layout:end layout:x="90" layout:y="370"/>
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-            </layout:listOfSpeciesReferenceGlyphs>
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-          <layout:reactionGlyph layout:id="Glyph__SrpR_degradation_interaction" layout:reaction="SrpR_degradation_interaction">
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-              <layout:position layout:x="600" layout:y="230"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
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-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="458" layout:y="200"/>
-                      <layout:end layout:x="610" layout:y="240"/>
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-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_degradation_interaction" layout:reaction="TetR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="890" layout:y="20"/>
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-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="560" layout:y="80"/>
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-          <layout:reactionGlyph layout:id="Glyph__LacI_degradation_interaction" layout:reaction="LacI_degradation_interaction">
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-                      <layout:start layout:x="470" layout:y="20"/>
-                      <layout:end layout:x="330" layout:y="20"/>
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-          <layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="338" layout:y="110"/>
-                      <layout:end layout:x="300" layout:y="210"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BetI_degradation_interaction" layout:reaction="BetI_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="940" layout:y="200"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BetI_degradation_interaction__substrate__BetI_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BetI_protein">
-                <layout:curve>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
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-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
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-        </annotation>
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-            <annotation>
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-              <ci> SrpR_protein </ci>
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-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
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-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
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-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
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-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000_bound.sm
deleted file mode 100644
index 543320e..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1/Circuit0x8E_TI_101to000_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_101to000.xml
-
-ctmc
-
-const int MAX_AMOUNT = 250;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.sm
deleted file mode 100644
index 2dd02fd..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 250;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 0;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml
deleted file mode 100644
index 2e9f85f..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-        </annotation>
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-    </listOfSpecies>
-    <listOfParameters>
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-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim24" species="TetR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim28">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim87" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim34">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="LacI_degradation_interaction" metaid="iBioSim88" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim35" species="LacI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim35">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI_protein </ci>
-            </apply>
-          </math>
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-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10_bound.sm
deleted file mode 100644
index 543320e..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to000_G1_10_10/Circuit0x8E_TI_101to000_G1_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_101to000.xml
-
-ctmc
-
-const int MAX_AMOUNT = 250;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.sm
deleted file mode 100644
index fd9eb3e..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 250;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 0;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml
deleted file mode 100644
index dc200de..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
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-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
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-          <apply>
-            <gt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
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-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
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-          </math>
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-        <annotation>
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-        </annotation>
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-            <annotation>
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim87" reversible="false">
-        <annotation>
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-        </annotation>
-              <listOfReactants>
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-            <annotation>
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-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
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-        <annotation>
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-        </annotation>
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diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011_bound.sm
deleted file mode 100644
index d5e3fa9..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1/Circuit0x8E_TI_101to011_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_101to011.xml
-
-ctmc
-
-const int MAX_AMOUNT = 250;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.csl
deleted file mode 100644
index d0b751b..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.csl
+++ /dev/null
@@ -1,6 +0,0 @@
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or below molecules
-
-P=? [ true U[0,1000] (YFP_protein <= 30) ]
-
-//P=? [ true U[0,1000] (YFP_protein < 30) ]
-
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.sm
deleted file mode 100644
index 11c219d..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 250;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 70;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 60;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 0;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml
deleted file mode 100644
index dc200de..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="360"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="250"/>
-                      <layout:end layout:x="90" layout:y="370"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
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-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
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-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/Inverter1_module/LacI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
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-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
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-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_Inverter1_module_sub__Inverter1_fc </ci>
-                      <ci> topModel_Inverter1_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_Inverter1_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__ko_f </ci>
-                      <ci> topModel_Inverter1_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_Inverter1_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_Inverter1_module_sub__kr_f </ci>
-                      <ci> topModel_Inverter1_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> LacI_protein </ci>
-                  </apply>
-                  <ci> topModel_Inverter1_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__iBioSim7" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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-              <rdf:Description rdf:about="#iBioSim7">
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-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
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-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
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-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10_bound.sm
deleted file mode 100644
index d5e3fa9..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_101to011_G1_10_10/Circuit0x8E_TI_101to011_G1_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_101to011.xml
-
-ctmc
-
-const int MAX_AMOUNT = 250;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = HIGH;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 250; // Initial amount 250
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 70; // Initial amount 70
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 0; // Initial amount 0
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.sm
deleted file mode 100644
index f46642d..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml
deleted file mode 100644
index 8ffe3ba..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="99" layout:y="5"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="748" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="328" layout:y="270"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__AmtR_protein" layout:species="AmtR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="50" layout:y="230"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="698" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction" layout:reaction="Ara_AraC_protein_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="139" layout:y="100"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Ara_AraC_protein_degradation_interaction__substrate__Ara_AraC_protein" layout:role="substrate" layout:speciesGlyph="Glyph__Ara_AraC_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="149" layout:y="20"/>
-                      <layout:end layout:x="149" layout:y="110"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="360"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
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-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="250"/>
-                      <layout:end layout:x="90" layout:y="370"/>
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-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__SrpR_degradation_interaction" layout:reaction="SrpR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="600" layout:y="230"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__SrpR_degradation_interaction__substrate__SrpR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__SrpR_protein">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="458" layout:y="200"/>
-                      <layout:end layout:x="610" layout:y="240"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR_degradation_interaction" layout:reaction="TetR_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="890" layout:y="20"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__TetR_degradation_interaction__substrate__TetR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__TetR_protein">
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-                      <layout:start layout:x="718" layout:y="20"/>
-                      <layout:end layout:x="900" layout:y="30"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__BM3R1_degradation_interaction" layout:reaction="BM3R1_degradation_interaction">
-            <layout:boundingBox>
-              <layout:position layout:x="560" layout:y="80"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__BM3R1_degradation_interaction__substrate__BM3R1_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BM3R1_protein">
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-                      <layout:start layout:x="452" layout:y="110"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
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-          <layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
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-                <layout:curve>
-                  <layout:listOfCurveSegments>
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-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim3">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim4" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim4">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim76" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim77" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim78" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
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-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim8">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> HlyIIR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__iBioSim10" reversible="false" sboTerm="SBO:0000589">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim10">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010_bound.sm
deleted file mode 100644
index 58947b2..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0/Circuit0x8E_TI_111to010_bound.sm
+++ /dev/null
@@ -1,441 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_111to010.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-//const int MAX_AMOUNT = 200;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.sm
deleted file mode 100644
index 01b10e4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 60;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 0;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml
deleted file mode 100644
index 8ffe3ba..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
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-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
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-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
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-            <layout:boundingBox>
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-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
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-        <layout:listOfCompartmentGlyphs>
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-              <layout:position layout:x="450" layout:y="0"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
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-    <listOfParameters>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
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-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
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-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
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-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim28">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
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-                    <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfProducts>
-          <speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim12">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-          <modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="TetR_protein">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim11">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </modifierSpeciesReference>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> topModel_BetIpart_module_sub__pTet </ci>
-                      <ci> topModel_BetIpart_module_sub__ko </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                </apply>
-                <ci> topModel_BetIpart_module_sub__nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__ko_f </ci>
-                      <ci> topModel_BetIpart_module_sub__ko_r </ci>
-                    </apply>
-                    <ci> topModel_BetIpart_module_sub__nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10_bound.sm
deleted file mode 100644
index 58947b2..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_111to010_G0_10_10_bound.sm
+++ /dev/null
@@ -1,441 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_111to010.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-//const int MAX_AMOUNT = 200;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = 0;
-const double LacI_protein = HIGH;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_G0csl.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to010_G0_10_10/Circuit0x8E_TI_G0csl.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.sm
deleted file mode 100644
index 4d5ce58..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml
deleted file mode 100644
index ff8e06a..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
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-    <listOfParameters>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
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-      <parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
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-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_f" metaid="topModel_Inverter2_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kr_r" metaid="topModel_Inverter2_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_f" metaid="topModel_Inverter2_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka_r" metaid="topModel_Inverter2_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_f" metaid="topModel_Inverter2_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko_r" metaid="topModel_Inverter2_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_f" metaid="topModel_Inverter2_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kao_r" metaid="topModel_Inverter2_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nc" metaid="topModel_Inverter2_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__nr" metaid="topModel_Inverter2_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ko" metaid="topModel_Inverter2_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__kb" metaid="topModel_Inverter2_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ng" metaid="topModel_Inverter2_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__np" metaid="topModel_Inverter2_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter2_module_sub__ka" metaid="topModel_Inverter2_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="SrpR_degradation_interaction" metaid="iBioSim80" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim23" species="SrpR_protein" stoichiometry="10">
-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim23">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/SrpR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
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-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> SrpR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="TetR_degradation_interaction" metaid="iBioSim81" reversible="false">
-        <annotation>
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-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
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-        </annotation>
-              <listOfReactants>
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-            <annotation>
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-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim24">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/TetR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="BM3R1_degradation_interaction" metaid="iBioSim84" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim27" species="BM3R1_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim27">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/BM3R1_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> BM3R1_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim85" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim28" species="PhlF_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim28">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim87" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim34">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="LacI_degradation_interaction" metaid="iBioSim88" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim35" species="LacI_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim35">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/LacI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim89" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
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-                      <ci> topModel_BetIpart_module_sub__kr_f </ci>
-                      <ci> topModel_BetIpart_module_sub__kr_r </ci>
-                    </apply>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> topModel_BetIpart_module_sub__nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim91" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim42" species="AmtR_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim42">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AmtR_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Ara_AraC_protein_degradation_interaction" metaid="iBioSim82" reversible="false">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#">
-                <mts:Interactions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim25" species="Ara_AraC_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-                <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-                  <rdf:Description rdf:about="#iBioSim25">
-                    <mts:Participations>
-                      <rdf:Bag>
-                        <rdf:li rdf:resource="http://www.async.utah.edu/topModel/Ara_AraC_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
-            </annotation>
-                    </speciesReference>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Ara_AraC_protein </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100_bound.sm
deleted file mode 100644
index 5f753b7..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0/Circuit0x8E_TI_111to100_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_111to100.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.sm
deleted file mode 100644
index e1a2e93..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.sm
+++ /dev/null
@@ -1,456 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: /Users/lukas/Lab/GitHub_Repositories/CaseStudies_StochasticModelChecking/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 7.5E-4; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter2_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter2_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter2_module_sub__ka = 0.25; // Activated production rate
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_Inverter1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_Inverter1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_Inverter1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_Inverter1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_Inverter1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_Inverter1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_Inverter1_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_Inverter1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_Inverter1_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_Inverter1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_Inverter1_module_sub__ka = 0.25; // Activated production rate
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
-const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
-const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
-const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
-const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
-
-// Species BM3R1_protein
-module BM3R1_protein
-
-  BM3R1_protein  :  int init 70;
-
-		// BM3R1_degradation_interaction
-		[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein' = BM3R1_protein - 10);
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] BM3R1_protein >= 0 -> (BM3R1_protein' = BM3R1_protein + 10);
-
-endmodule
-
-// Species HlyIIR_protein
-module HlyIIR_protein
-
-  HlyIIR_protein  :  int init 310;
-
-		// HlyIIR_degradation_interaction
-		[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein' = HlyIIR_protein - 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein >= 0 -> (HlyIIR_protein' = HlyIIR_protein + 10);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// YFP_degradation_interaction
-		[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein' = YFP_protein - 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein >= 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species SrpR_protein
-module SrpR_protein
-
-  SrpR_protein  :  int init 0;
-
-		// SrpR_degradation_interaction
-		[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein' = SrpR_protein - 10);
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] SrpR_protein >= 0 -> (SrpR_protein' = SrpR_protein + 10);
-
-endmodule
-
-// Species Ara_AraC_protein
-module Ara_AraC_protein
-
-  Ara_AraC_protein  :  int init 0;
-
-		// Ara_AraC_protein_degradation_interaction
-		[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 9 -> (Ara_AraC_protein' = Ara_AraC_protein - 10);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// LacI_degradation_interaction
-		[LacI_degradation_interaction] LacI_protein > 9 -> (LacI_protein' = LacI_protein - 10);
-
-endmodule
-
-// Species BetI_protein
-module BetI_protein
-
-  BetI_protein  :  int init 70;
-
-		// BetI_degradation_interaction
-		[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein' = BetI_protein - 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein >= 0 -> (BetI_protein' = BetI_protein + 10);
-
-endmodule
-
-// Species PhlF_protein
-module PhlF_protein
-
-  PhlF_protein  :  int init 70;
-
-		// PhlF_degradation_interaction
-		[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein' = PhlF_protein - 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein >= 0 -> (PhlF_protein' = PhlF_protein + 10);
-
-endmodule
-
-// Species AmtR_protein
-module AmtR_protein
-
-  AmtR_protein  :  int init 250;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein >= 0 -> (AmtR_protein' = AmtR_protein + 10);
-		// AmtR_degradation_interaction
-		[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein' = AmtR_protein - 10);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// TetR_degradation_interaction
-		[TetR_degradation_interaction] TetR_protein > 9 -> (TetR_protein' = TetR_protein - 10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-module topModel_PhlFpart_module_sub__pAmtR
-
-  topModel_PhlFpart_module_sub__pAmtR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-module topModel_PhlFpart_module_sub__pSrpR
-
-  topModel_PhlFpart_module_sub__pSrpR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-module topModel_YFPpart_module_sub__pBetI
-
-  topModel_YFPpart_module_sub__pBetI  :  int init 2;
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-module topModel_YFPpart_module_sub__pPhlF
-
-  topModel_YFPpart_module_sub__pPhlF  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-  topModel_Inverter2_module_sub__Inverter2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-module topModel_AmtRpart_module_sub__pBAD
-
-  topModel_AmtRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-  topModel_AmtRpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-module topModel_HlyIIRpart_module_sub__pTet
-
-  topModel_HlyIIRpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-module topModel_HlyIIRpart_module_sub__pBAD
-
-  topModel_HlyIIRpart_module_sub__pBAD  :  int init 2;
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-  topModel_Inverter1_module_sub__Inverter1_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-module topModel_BetIpart_module_sub__pHlyIIR
-
-  topModel_BetIpart_module_sub__pHlyIIR  :  int init 2;
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-module topModel_BetIpart_module_sub__pTet
-
-  topModel_BetIpart_module_sub__pTet  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// SrpR_degradation_interaction: 10 SrpR_protein -> 
-		[SrpR_degradation_interaction] (kd * SrpR_protein) > 0 -> (kd * SrpR_protein) : true;
-
-		// TetR_degradation_interaction: 10 TetR_protein -> 
-		[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// BM3R1_degradation_interaction: 10 BM3R1_protein -> 
-		[BM3R1_degradation_interaction] (kd * BM3R1_protein) > 0 -> (kd * BM3R1_protein) : true;
-
-		// PhlF_degradation_interaction: 10 PhlF_protein -> 
-		[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> (kd * PhlF_protein) : true;
-
-		// YFP_degradation_interaction: 10 YFP_protein -> 
-		[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// LacI_degradation_interaction: 10 LacI_protein -> 
-		[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// HlyIIR_degradation_interaction: 10 HlyIIR_protein -> 
-		[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> (kd * HlyIIR_protein) : true;
-
-		// BetI_degradation_interaction: 10 BetI_protein -> 
-		[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> (kd * BetI_protein) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * SrpR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> 10 PhlF_protein
-		[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> 10 YFP_protein
-		[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) : true;
-
-		// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> 10 SrpR_protein
-		[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc * topModel_Inverter2_module_sub__ko) * topModel_Inverter2_module_sub__ko_f) / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr) / ((1 + ((topModel_Inverter2_module_sub__ko_f / topModel_Inverter2_module_sub__ko_r) * topModel_Inverter2_module_sub__nr)) + pow(((topModel_Inverter2_module_sub__kr_f / topModel_Inverter2_module_sub__kr_r) * BM3R1_protein) , topModel_Inverter2_module_sub__nc))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD * (((kb * (ko_f / ko_r)) * nr) + (((ka * (kao_f / kao_r)) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) / ((1 + ((ko_f / ko_r) * nr)) + (((kao_f / kao_r) * nr) * pow(((ka_f / ka_r) * Ara_AraC_protein) , nc)))) : true;
-
-		// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> 10 AmtR_protein
-		[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
-
-		// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> 10 HlyIIR_protein
-		[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) : true;
-
-		// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> 10 BM3R1_protein
-		[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc * topModel_Inverter1_module_sub__ko) * topModel_Inverter1_module_sub__ko_f) / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr) / ((1 + ((topModel_Inverter1_module_sub__ko_f / topModel_Inverter1_module_sub__ko_r) * topModel_Inverter1_module_sub__nr)) + pow(((topModel_Inverter1_module_sub__kr_f / topModel_Inverter1_module_sub__kr_r) * LacI_protein) , topModel_Inverter1_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> 10 BetI_protein
-		[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) : true;
-
-		// AmtR_degradation_interaction: 10 AmtR_protein -> 
-		[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> (kd * AmtR_protein) : true;
-
-		// Ara_AraC_protein_degradation_interaction: 10 Ara_AraC_protein -> 
-		[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> (kd * Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 5: Ara_AraC_protein
-rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
-// Reward 6: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 10: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml
deleted file mode 100644
index ff8e06a..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10.xml
+++ /dev/null
@@ -1,2620 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModel" metaid="iBioSim7" name="Created by iBioSim flatten routine">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="http://www.async.utah.edu/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
-    </annotation>
-      <fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="721" layout:y="364"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="630" layout:y="390"/>
-                      <layout:end layout:x="746" layout:y="384"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__BM3R1_protein" layout:species="BM3R1_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="432" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="318" layout:y="90"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="610" layout:y="370"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__SrpR_protein" layout:species="SrpR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="438" layout:y="180"/>
-              <layout:dimensions layout:height="40" layout:width="40"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
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-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_f" metaid="topModel_Inverter1_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kr_r" metaid="topModel_Inverter1_module_sub__iBioSim9" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_f" metaid="topModel_Inverter1_module_sub__iBioSim10" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka_r" metaid="topModel_Inverter1_module_sub__iBioSim11" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_f" metaid="topModel_Inverter1_module_sub__iBioSim12" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko_r" metaid="topModel_Inverter1_module_sub__iBioSim13" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_f" metaid="topModel_Inverter1_module_sub__iBioSim14" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kao_r" metaid="topModel_Inverter1_module_sub__iBioSim15" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nc" metaid="topModel_Inverter1_module_sub__iBioSim16" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__nr" metaid="topModel_Inverter1_module_sub__iBioSim17" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ko" metaid="topModel_Inverter1_module_sub__iBioSim18" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__kb" metaid="topModel_Inverter1_module_sub__iBioSim19" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ng" metaid="topModel_Inverter1_module_sub__iBioSim20" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__np" metaid="topModel_Inverter1_module_sub__iBioSim21" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_Inverter1_module_sub__ka" metaid="topModel_Inverter1_module_sub__iBioSim22" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <lt/>
-            <ci> YFP_protein </ci>
-            <cn type="integer"> 30 </cn>
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-        </math>
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-    </listOfConstraints>
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-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <times/>
-              <ci> kd </ci>
-              <ci> PhlF_protein </ci>
-            </apply>
-          </math>
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-      </reaction>
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-        <annotation>
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-        </annotation>
-              <listOfReactants>
-          <speciesReference constant="true" metaid="iBioSim34" species="YFP_protein" stoichiometry="10">
-            <annotation>
-              <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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-          <math xmlns="http://www.w3.org/1998/Math/MathML">
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-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
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-        <annotation>
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-              <ci> LacI_protein </ci>
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diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10_bound.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10_bound.sm
deleted file mode 100644
index 5f753b7..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_111to100_G0_10_10_bound.sm
+++ /dev/null
@@ -1,439 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: Circuit0x8E_TI_111to100.xml
-
-ctmc
-
-const int MAX_AMOUNT = 310;
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model inputs
-const HIGH = 60;
-const double TetR_protein = HIGH;
-const double LacI_protein = 0;
-const double Ara_AraC_protein = 0;
-
-
-// Manually added parameters
-const double kb = 0.0001;
-const double ko_f = 0.05;
-const double ko_r = 1;
-const double nr = 30;
-const double ka = 0.25;
-const double ka_f = 0.25;
-const double ka_r = 1;
-
-const double kao_f = 1;
-const double kao_r = 1;
-
-// Model parameters
-const double kd = 0.00075; // kd
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double nc = 2; // nc
-const double topModel_PhlFpart_module_sub__kr_f = 0.5; // topModel_PhlFpart_module_sub__kr_f
-const double topModel_PhlFpart_module_sub__kr_r = 1; // topModel_PhlFpart_module_sub__kr_r
-const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // topModel_PhlFpart_module_sub__ka_f
-const double topModel_PhlFpart_module_sub__ka_r = 1; // topModel_PhlFpart_module_sub__ka_r
-const double topModel_PhlFpart_module_sub__ko_f = 0.033; // topModel_PhlFpart_module_sub__ko_f
-const double topModel_PhlFpart_module_sub__ko_r = 1; // topModel_PhlFpart_module_sub__ko_r
-const double topModel_PhlFpart_module_sub__kao_f = 1; // topModel_PhlFpart_module_sub__kao_f
-const double topModel_PhlFpart_module_sub__kao_r = 1; // topModel_PhlFpart_module_sub__kao_r
-const double topModel_PhlFpart_module_sub__nc = 2; // topModel_PhlFpart_module_sub__nc
-const double topModel_PhlFpart_module_sub__nr = 30; // topModel_PhlFpart_module_sub__nr
-const double topModel_PhlFpart_module_sub__ko = 0.05; // topModel_PhlFpart_module_sub__ko
-const double topModel_PhlFpart_module_sub__kb = 0.0001; // topModel_PhlFpart_module_sub__kb
-const double topModel_PhlFpart_module_sub__ng = 2; // topModel_PhlFpart_module_sub__ng
-const double topModel_PhlFpart_module_sub__np = 10; // topModel_PhlFpart_module_sub__np
-const double topModel_PhlFpart_module_sub__ka = 0.25; // topModel_PhlFpart_module_sub__ka
-const double topModel_YFPpart_module_sub__kr_f = 0.5; // topModel_YFPpart_module_sub__kr_f
-const double topModel_YFPpart_module_sub__kr_r = 1; // topModel_YFPpart_module_sub__kr_r
-const double topModel_YFPpart_module_sub__ka_f = 0.0033; // topModel_YFPpart_module_sub__ka_f
-const double topModel_YFPpart_module_sub__ka_r = 1; // topModel_YFPpart_module_sub__ka_r
-const double topModel_YFPpart_module_sub__ko_f = 0.033; // topModel_YFPpart_module_sub__ko_f
-const double topModel_YFPpart_module_sub__ko_r = 1; // topModel_YFPpart_module_sub__ko_r
-const double topModel_YFPpart_module_sub__kao_f = 1; // topModel_YFPpart_module_sub__kao_f
-const double topModel_YFPpart_module_sub__kao_r = 1; // topModel_YFPpart_module_sub__kao_r
-const double topModel_YFPpart_module_sub__nc = 2; // topModel_YFPpart_module_sub__nc
-const double topModel_YFPpart_module_sub__nr = 30; // topModel_YFPpart_module_sub__nr
-const double topModel_YFPpart_module_sub__ko = 0.05; // topModel_YFPpart_module_sub__ko
-const double topModel_YFPpart_module_sub__kb = 0.0001; // topModel_YFPpart_module_sub__kb
-const double topModel_YFPpart_module_sub__ng = 2; // topModel_YFPpart_module_sub__ng
-const double topModel_YFPpart_module_sub__np = 10; // topModel_YFPpart_module_sub__np
-const double topModel_YFPpart_module_sub__ka = 0.25; // topModel_YFPpart_module_sub__ka
-const double topModel_Inverter2_module_sub__kr_f = 0.5; // topModel_Inverter2_module_sub__kr_f
-const double topModel_Inverter2_module_sub__kr_r = 1; // topModel_Inverter2_module_sub__kr_r
-const double topModel_Inverter2_module_sub__ka_f = 0.0033; // topModel_Inverter2_module_sub__ka_f
-const double topModel_Inverter2_module_sub__ka_r = 1; // topModel_Inverter2_module_sub__ka_r
-const double topModel_Inverter2_module_sub__ko_f = 0.033; // topModel_Inverter2_module_sub__ko_f
-const double topModel_Inverter2_module_sub__ko_r = 1; // topModel_Inverter2_module_sub__ko_r
-const double topModel_Inverter2_module_sub__kao_f = 1; // topModel_Inverter2_module_sub__kao_f
-const double topModel_Inverter2_module_sub__kao_r = 1; // topModel_Inverter2_module_sub__kao_r
-const double topModel_Inverter2_module_sub__nc = 2; // topModel_Inverter2_module_sub__nc
-const double topModel_Inverter2_module_sub__nr = 30; // topModel_Inverter2_module_sub__nr
-const double topModel_Inverter2_module_sub__ko = 0.05; // topModel_Inverter2_module_sub__ko
-const double topModel_Inverter2_module_sub__kb = 0.0001; // topModel_Inverter2_module_sub__kb
-const double topModel_Inverter2_module_sub__ng = 2; // topModel_Inverter2_module_sub__ng
-const double topModel_Inverter2_module_sub__np = 10; // topModel_Inverter2_module_sub__np
-const double topModel_Inverter2_module_sub__ka = 0.25; // topModel_Inverter2_module_sub__ka
-const double topModel_AmtRpart_module_sub__kr_f = 0.5; // topModel_AmtRpart_module_sub__kr_f
-const double topModel_AmtRpart_module_sub__kr_r = 1; // topModel_AmtRpart_module_sub__kr_r
-const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // topModel_AmtRpart_module_sub__ka_f
-const double topModel_AmtRpart_module_sub__ka_r = 1; // topModel_AmtRpart_module_sub__ka_r
-const double topModel_AmtRpart_module_sub__ko_f = 0.033; // topModel_AmtRpart_module_sub__ko_f
-const double topModel_AmtRpart_module_sub__ko_r = 1; // topModel_AmtRpart_module_sub__ko_r
-const double topModel_AmtRpart_module_sub__kao_f = 1; // topModel_AmtRpart_module_sub__kao_f
-const double topModel_AmtRpart_module_sub__kao_r = 1; // topModel_AmtRpart_module_sub__kao_r
-const double topModel_AmtRpart_module_sub__nc = 2; // topModel_AmtRpart_module_sub__nc
-const double topModel_AmtRpart_module_sub__nr = 30; // topModel_AmtRpart_module_sub__nr
-const double topModel_AmtRpart_module_sub__ko = 0.05; // topModel_AmtRpart_module_sub__ko
-const double topModel_AmtRpart_module_sub__kb = 0.0001; // topModel_AmtRpart_module_sub__kb
-const double topModel_AmtRpart_module_sub__ng = 2; // topModel_AmtRpart_module_sub__ng
-const double topModel_AmtRpart_module_sub__np = 10; // topModel_AmtRpart_module_sub__np
-const double topModel_AmtRpart_module_sub__ka = 0.25; // topModel_AmtRpart_module_sub__ka
-const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // topModel_HlyIIRpart_module_sub__kr_f
-const double topModel_HlyIIRpart_module_sub__kr_r = 1; // topModel_HlyIIRpart_module_sub__kr_r
-const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // topModel_HlyIIRpart_module_sub__ka_f
-const double topModel_HlyIIRpart_module_sub__ka_r = 1; // topModel_HlyIIRpart_module_sub__ka_r
-const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // topModel_HlyIIRpart_module_sub__ko_f
-const double topModel_HlyIIRpart_module_sub__ko_r = 1; // topModel_HlyIIRpart_module_sub__ko_r
-const double topModel_HlyIIRpart_module_sub__kao_f = 1; // topModel_HlyIIRpart_module_sub__kao_f
-const double topModel_HlyIIRpart_module_sub__kao_r = 1; // topModel_HlyIIRpart_module_sub__kao_r
-const double topModel_HlyIIRpart_module_sub__nc = 2; // topModel_HlyIIRpart_module_sub__nc
-const double topModel_HlyIIRpart_module_sub__nr = 30; // topModel_HlyIIRpart_module_sub__nr
-const double topModel_HlyIIRpart_module_sub__ko = 0.05; // topModel_HlyIIRpart_module_sub__ko
-const double topModel_HlyIIRpart_module_sub__kb = 0.0001; // topModel_HlyIIRpart_module_sub__kb
-const double topModel_HlyIIRpart_module_sub__ng = 2; // topModel_HlyIIRpart_module_sub__ng
-const double topModel_HlyIIRpart_module_sub__np = 10; // topModel_HlyIIRpart_module_sub__np
-const double topModel_HlyIIRpart_module_sub__ka = 0.25; // topModel_HlyIIRpart_module_sub__ka
-const double topModel_Inverter1_module_sub__kr_f = 0.5; // topModel_Inverter1_module_sub__kr_f
-const double topModel_Inverter1_module_sub__kr_r = 1; // topModel_Inverter1_module_sub__kr_r
-const double topModel_Inverter1_module_sub__ka_f = 0.0033; // topModel_Inverter1_module_sub__ka_f
-const double topModel_Inverter1_module_sub__ka_r = 1; // topModel_Inverter1_module_sub__ka_r
-const double topModel_Inverter1_module_sub__ko_f = 0.033; // topModel_Inverter1_module_sub__ko_f
-const double topModel_Inverter1_module_sub__ko_r = 1; // topModel_Inverter1_module_sub__ko_r
-const double topModel_Inverter1_module_sub__kao_f = 1; // topModel_Inverter1_module_sub__kao_f
-const double topModel_Inverter1_module_sub__kao_r = 1; // topModel_Inverter1_module_sub__kao_r
-const double topModel_Inverter1_module_sub__nc = 2; // topModel_Inverter1_module_sub__nc
-const double topModel_Inverter1_module_sub__nr = 30; // topModel_Inverter1_module_sub__nr
-const double topModel_Inverter1_module_sub__ko = 0.05; // topModel_Inverter1_module_sub__ko
-const double topModel_Inverter1_module_sub__kb = 0.0001; // topModel_Inverter1_module_sub__kb
-const double topModel_Inverter1_module_sub__ng = 2; // topModel_Inverter1_module_sub__ng
-const double topModel_Inverter1_module_sub__np = 10; // topModel_Inverter1_module_sub__np
-const double topModel_Inverter1_module_sub__ka = 0.25; // topModel_Inverter1_module_sub__ka
-const double topModel_BetIpart_module_sub__kr_f = 0.5; // topModel_BetIpart_module_sub__kr_f
-const double topModel_BetIpart_module_sub__kr_r = 1; // topModel_BetIpart_module_sub__kr_r
-const double topModel_BetIpart_module_sub__ka_f = 0.0033; // topModel_BetIpart_module_sub__ka_f
-const double topModel_BetIpart_module_sub__ka_r = 1; // topModel_BetIpart_module_sub__ka_r
-const double topModel_BetIpart_module_sub__ko_f = 0.033; // topModel_BetIpart_module_sub__ko_f
-const double topModel_BetIpart_module_sub__ko_r = 1; // topModel_BetIpart_module_sub__ko_r
-const double topModel_BetIpart_module_sub__kao_f = 1; // topModel_BetIpart_module_sub__kao_f
-const double topModel_BetIpart_module_sub__kao_r = 1; // topModel_BetIpart_module_sub__kao_r
-const double topModel_BetIpart_module_sub__nc = 2; // topModel_BetIpart_module_sub__nc
-const double topModel_BetIpart_module_sub__nr = 30; // topModel_BetIpart_module_sub__nr
-const double topModel_BetIpart_module_sub__ko = 0.05; // topModel_BetIpart_module_sub__ko
-const double topModel_BetIpart_module_sub__kb = 0.0001; // topModel_BetIpart_module_sub__kb
-const double topModel_BetIpart_module_sub__ng = 2; // topModel_BetIpart_module_sub__ng
-const double topModel_BetIpart_module_sub__np = 10; // topModel_BetIpart_module_sub__np
-const double topModel_BetIpart_module_sub__ka = 0.25; // topModel_BetIpart_module_sub__ka
-
-// Species BM3R1_protein
-const int BM3R1_protein_MAX = MAX_AMOUNT;
-module BM3R1_protein
-
-	BM3R1_protein : [0..BM3R1_protein_MAX] init 70; // Initial amount 70
-
-	// BM3R1_degradation_interaction
-	[BM3R1_degradation_interaction] BM3R1_protein > 9 -> (BM3R1_protein'=BM3R1_protein-10);
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction]  BM3R1_protein <= BM3R1_protein_MAX-10 -> (BM3R1_protein'=BM3R1_protein+10);
-
-endmodule
-
-// Species HlyIIR_protein
-const int HlyIIR_protein_MAX = MAX_AMOUNT;
-module HlyIIR_protein
-
-	HlyIIR_protein : [0..HlyIIR_protein_MAX] init 310; // Initial amount 310
-
-	// HlyIIR_degradation_interaction
-	[HlyIIR_degradation_interaction] HlyIIR_protein > 9 -> (HlyIIR_protein'=HlyIIR_protein-10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1]  HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
-
-endmodule
-
-// Species YFP_protein
-const int YFP_protein_MAX = MAX_AMOUNT;
-module YFP_protein
-
-	YFP_protein : [0..YFP_protein_MAX] init 0; // Initial amount 0
-
-	// YFP_degradation_interaction
-	[YFP_degradation_interaction] YFP_protein > 9 -> (YFP_protein'=YFP_protein-10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1]  YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
-
-endmodule
-
-// Species SrpR_protein
-const int SrpR_protein_MAX = MAX_AMOUNT;
-module SrpR_protein
-
-	SrpR_protein : [0..SrpR_protein_MAX] init 0; // Initial amount 0
-
-	// SrpR_degradation_interaction
-	[SrpR_degradation_interaction] SrpR_protein > 9 -> (SrpR_protein'=SrpR_protein-10);
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction]  SrpR_protein <= SrpR_protein_MAX-10 -> (SrpR_protein'=SrpR_protein+10);
-
-endmodule
-
-// Species BetI_protein
-const int BetI_protein_MAX = MAX_AMOUNT;
-module BetI_protein
-
-	BetI_protein : [0..BetI_protein_MAX] init 70; // Initial amount 70
-
-	// BetI_degradation_interaction
-	[BetI_degradation_interaction] BetI_protein > 9 -> (BetI_protein'=BetI_protein-10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1]  BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
-
-endmodule
-
-// Species PhlF_protein
-const int PhlF_protein_MAX = MAX_AMOUNT;
-module PhlF_protein
-
-	PhlF_protein : [0..PhlF_protein_MAX] init 70; // Initial amount 70
-
-	// PhlF_degradation_interaction
-	[PhlF_degradation_interaction] PhlF_protein > 9 -> (PhlF_protein'=PhlF_protein-10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1]  PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
-
-endmodule
-
-// Species AmtR_protein
-const int AmtR_protein_MAX = MAX_AMOUNT;
-module AmtR_protein
-
-	AmtR_protein : [0..AmtR_protein_MAX] init 250; // Initial amount 250
-
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1]  AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
-	// AmtR_degradation_interaction
-	[AmtR_degradation_interaction] AmtR_protein > 9 -> (AmtR_protein'=AmtR_protein-10);
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pAmtR
-const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pAmtR
-
-	topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_PhlFpart_module_sub__pSrpR
-const int topModel_PhlFpart_module_sub__pSrpR_MAX = MAX_AMOUNT;
-module topModel_PhlFpart_module_sub__pSrpR
-
-	topModel_PhlFpart_module_sub__pSrpR : [0..topModel_PhlFpart_module_sub__pSrpR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pBetI
-const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pBetI
-
-	topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_YFPpart_module_sub__pPhlF
-const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
-module topModel_YFPpart_module_sub__pPhlF
-
-	topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter2_module_sub__Inverter2_fc
-const int topModel_Inverter2_module_sub__Inverter2_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter2_module_sub__Inverter2_fc
-
-	topModel_Inverter2_module_sub__Inverter2_fc : [0..topModel_Inverter2_module_sub__Inverter2_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pBAD
-const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pBAD
-
-	topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_AmtRpart_module_sub__pHlyIIR
-const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_AmtRpart_module_sub__pHlyIIR
-
-	topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pTet
-const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pTet
-
-	topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_HlyIIRpart_module_sub__pBAD
-const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
-module topModel_HlyIIRpart_module_sub__pBAD
-
-	topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_Inverter1_module_sub__Inverter1_fc
-const int topModel_Inverter1_module_sub__Inverter1_fc_MAX = MAX_AMOUNT;
-module topModel_Inverter1_module_sub__Inverter1_fc
-
-	topModel_Inverter1_module_sub__Inverter1_fc : [0..topModel_Inverter1_module_sub__Inverter1_fc_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pHlyIIR
-const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pHlyIIR
-
-	topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species topModel_BetIpart_module_sub__pTet
-const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
-module topModel_BetIpart_module_sub__pTet
-
-	topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// SrpR_degradation_interaction: SrpR_protein ->
-	[SrpR_degradation_interaction] (kd*SrpR_protein) > 0 -> (kd*SrpR_protein) : true;
-	// TetR_degradation_interaction: TetR_protein ->
-	[TetR_degradation_interaction] (kd*TetR_protein) > 0 -> (kd*TetR_protein) : true;
-	// BM3R1_degradation_interaction: BM3R1_protein ->
-	[BM3R1_degradation_interaction] (kd*BM3R1_protein) > 0 -> (kd*BM3R1_protein) : true;
-	// PhlF_degradation_interaction: PhlF_protein ->
-	[PhlF_degradation_interaction] (kd*PhlF_protein) > 0 -> (kd*PhlF_protein) : true;
-	// YFP_degradation_interaction: YFP_protein ->
-	[YFP_degradation_interaction] (kd*YFP_protein) > 0 -> (kd*YFP_protein) : true;
-	// LacI_degradation_interaction: LacI_protein ->
-	[LacI_degradation_interaction] (kd*LacI_protein) > 0 -> (kd*LacI_protein) : true;
-	// HlyIIR_degradation_interaction: HlyIIR_protein ->
-	[HlyIIR_degradation_interaction] (kd*HlyIIR_protein) > 0 -> (kd*HlyIIR_protein) : true;
-	// BetI_degradation_interaction: BetI_protein ->
-	[BetI_degradation_interaction] (kd*BetI_protein) > 0 -> (kd*BetI_protein) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pAmtR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*SrpR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1:  -> PhlF_protein
-	[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) > 0 -> (((((topModel_PhlFpart_module_sub__pSrpR*topModel_PhlFpart_module_sub__ko)*topModel_PhlFpart_module_sub__ko_f)/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr)/((1+((topModel_PhlFpart_module_sub__ko_f/topModel_PhlFpart_module_sub__ko_r)*topModel_PhlFpart_module_sub__nr))+(func(pow,((topModel_PhlFpart_module_sub__kr_f/topModel_PhlFpart_module_sub__kr_r)*AmtR_protein),topModel_PhlFpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_0:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pBetI*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*PhlF_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_YFPpart_module_sub__YFP_protein_interaction_1:  -> YFP_protein
-	[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) > 0 -> (((((topModel_YFPpart_module_sub__pPhlF*topModel_YFPpart_module_sub__ko)*topModel_YFPpart_module_sub__ko_f)/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr)/((1+((topModel_YFPpart_module_sub__ko_f/topModel_YFPpart_module_sub__ko_r)*topModel_YFPpart_module_sub__nr))+(func(pow,((topModel_YFPpart_module_sub__kr_f/topModel_YFPpart_module_sub__kr_r)*BetI_protein),topModel_YFPpart_module_sub__nc)))) : true;
-	// topModel_Inverter2_module_sub__SrpR_protein_interaction:  -> SrpR_protein
-	[topModel_Inverter2_module_sub__SrpR_protein_interaction] (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) > 0 -> (((((topModel_Inverter2_module_sub__Inverter2_fc*topModel_Inverter2_module_sub__ko)*topModel_Inverter2_module_sub__ko_f)/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr)/((1+((topModel_Inverter2_module_sub__ko_f/topModel_Inverter2_module_sub__ko_r)*topModel_Inverter2_module_sub__nr))+(func(pow,((topModel_Inverter2_module_sub__kr_f/topModel_Inverter2_module_sub__kr_r)*BM3R1_protein),topModel_Inverter2_module_sub__nc)))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) > 0 -> ((topModel_AmtRpart_module_sub__pBAD*(((kb*(ko_f/ko_r))*nr)+(((ka*(kao_f/kao_r))*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc)))))/((1+((ko_f/ko_r)*nr))+(((kao_f/kao_r)*nr)*(func(pow,((ka_f/ka_r)*Ara_AraC_protein),nc))))) : true;
-	// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1:  -> AmtR_protein
-	[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) > 0 -> (((((topModel_AmtRpart_module_sub__pHlyIIR*topModel_AmtRpart_module_sub__ko)*topModel_AmtRpart_module_sub__ko_f)/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr)/((1+((topModel_AmtRpart_module_sub__ko_f/topModel_AmtRpart_module_sub__ko_r)*topModel_AmtRpart_module_sub__nr))+(func(pow,((topModel_AmtRpart_module_sub__kr_f/topModel_AmtRpart_module_sub__kr_r)*HlyIIR_protein),topModel_AmtRpart_module_sub__nc)))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) > 0 -> ((topModel_HlyIIRpart_module_sub__pTet*((((topModel_HlyIIRpart_module_sub__kb*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)+((((topModel_HlyIIRpart_module_sub__ka*topModel_HlyIIRpart_module_sub__kao_f)/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc)))))/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(((topModel_HlyIIRpart_module_sub__kao_f/topModel_HlyIIRpart_module_sub__kao_r)*topModel_HlyIIRpart_module_sub__nr)*(func(pow,((topModel_HlyIIRpart_module_sub__ka_f/topModel_HlyIIRpart_module_sub__ka_r)*Ara_AraC_protein),topModel_HlyIIRpart_module_sub__nc))))) : true;
-	// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1:  -> HlyIIR_protein
-	[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((((topModel_HlyIIRpart_module_sub__pBAD*topModel_HlyIIRpart_module_sub__ko)*topModel_HlyIIRpart_module_sub__ko_f)/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr)/((1+((topModel_HlyIIRpart_module_sub__ko_f/topModel_HlyIIRpart_module_sub__ko_r)*topModel_HlyIIRpart_module_sub__nr))+(func(pow,((topModel_HlyIIRpart_module_sub__kr_f/topModel_HlyIIRpart_module_sub__kr_r)*TetR_protein),topModel_HlyIIRpart_module_sub__nc)))) : true;
-	// topModel_Inverter1_module_sub__BM3R1_protein_interaction:  -> BM3R1_protein
-	[topModel_Inverter1_module_sub__BM3R1_protein_interaction] (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) > 0 -> (((((topModel_Inverter1_module_sub__Inverter1_fc*topModel_Inverter1_module_sub__ko)*topModel_Inverter1_module_sub__ko_f)/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr)/((1+((topModel_Inverter1_module_sub__ko_f/topModel_Inverter1_module_sub__ko_r)*topModel_Inverter1_module_sub__nr))+(func(pow,((topModel_Inverter1_module_sub__kr_f/topModel_Inverter1_module_sub__kr_r)*LacI_protein),topModel_Inverter1_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_0:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pHlyIIR*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*HlyIIR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// topModel_BetIpart_module_sub__BetI_protein_interaction_1:  -> BetI_protein
-	[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) > 0 -> (((((topModel_BetIpart_module_sub__pTet*topModel_BetIpart_module_sub__ko)*topModel_BetIpart_module_sub__ko_f)/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr)/((1+((topModel_BetIpart_module_sub__ko_f/topModel_BetIpart_module_sub__ko_r)*topModel_BetIpart_module_sub__nr))+(func(pow,((topModel_BetIpart_module_sub__kr_f/topModel_BetIpart_module_sub__kr_r)*TetR_protein),topModel_BetIpart_module_sub__nc)))) : true;
-	// AmtR_degradation_interaction: AmtR_protein ->
-	[AmtR_degradation_interaction] (kd*AmtR_protein) > 0 -> (kd*AmtR_protein) : true;
-	// Ara_AraC_protein_degradation_interaction: Ara_AraC_protein ->
-	[Ara_AraC_protein_degradation_interaction] (kd*Ara_AraC_protein) > 0 -> (kd*Ara_AraC_protein) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: BM3R1_protein
-rewards "BM3R1_protein" true : BM3R1_protein; endrewards
-// Reward 2: HlyIIR_protein
-rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: SrpR_protein
-rewards "SrpR_protein" true : SrpR_protein; endrewards
-// Reward 7: BetI_protein
-rewards "BetI_protein" true : BetI_protein; endrewards
-// Reward 8: PhlF_protein
-rewards "PhlF_protein" true : PhlF_protein; endrewards
-// Reward 9: AmtR_protein
-rewards "AmtR_protein" true : AmtR_protein; endrewards
-// Reward 11: topModel_PhlFpart_module_sub__pAmtR
-rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
-// Reward 12: topModel_PhlFpart_module_sub__pSrpR
-rewards "topModel_PhlFpart_module_sub__pSrpR" true : topModel_PhlFpart_module_sub__pSrpR; endrewards
-// Reward 13: topModel_YFPpart_module_sub__pBetI
-rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
-// Reward 14: topModel_YFPpart_module_sub__pPhlF
-rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
-// Reward 15: topModel_Inverter2_module_sub__Inverter2_fc
-rewards "topModel_Inverter2_module_sub__Inverter2_fc" true : topModel_Inverter2_module_sub__Inverter2_fc; endrewards
-// Reward 16: topModel_AmtRpart_module_sub__pBAD
-rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
-// Reward 17: topModel_AmtRpart_module_sub__pHlyIIR
-rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
-// Reward 18: topModel_HlyIIRpart_module_sub__pTet
-rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
-// Reward 19: topModel_HlyIIRpart_module_sub__pBAD
-rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
-// Reward 20: topModel_Inverter1_module_sub__Inverter1_fc
-rewards "topModel_Inverter1_module_sub__Inverter1_fc" true : topModel_Inverter1_module_sub__Inverter1_fc; endrewards
-// Reward 21: topModel_BetIpart_module_sub__pHlyIIR
-rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
-// Reward 22: topModel_BetIpart_module_sub__pTet
-rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
diff --git a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_G0csl.csl b/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_G0csl.csl
deleted file mode 100644
index 46fa7d4..0000000
--- a/GeneticCircuits/Circuit0x8E/Circuit0x8E_TI_111to100_G0_10_10/Circuit0x8E_TI_G0csl.csl
+++ /dev/null
@@ -1,4 +0,0 @@
-
-// Hazard for transitions where YFP should remain low: the probability that YFP reaches 30 or above molecules
-
-P=? [ true U[0,1000] (YFP_protein >= 10) ]
diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml
deleted file mode 100755
index 3983833..0000000
--- a/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml
+++ /dev/null
@@ -1,547 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" distrib:required="true" fbc:required="false" layout:required="false" level="2" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:distrib="http://www.sbml.org/sbml/level3/version1/distrib/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="dual_feedback_oscillator" metaid="iBioSim32">
-    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
-      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
-      <comp:port comp:id="output__AraC" comp:idRef="AraC" sboTerm="SBO:0000601"/>
-      <comp:port comp:id="Degradation_AraC" comp:idRef="Degradation_AraC" sboTerm="SBO:0000601"/>
-      <comp:port comp:id="output__LacI" comp:idRef="LacI" sboTerm="SBO:0000601"/>
-      <comp:port comp:id="Degradation_LacI" comp:idRef="Degradation_LacI" sboTerm="SBO:0000601"/>
-      <comp:port comp:idRef="Cell" sboTerm="SBO:0000601"/>
-    </comp:listOfPorts>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__constraint0" layout:metaidRef="constraint0">
-            <layout:boundingBox>
-              <layout:position layout:x="350" layout:y="70"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__AraC" layout:id="Glyph__constraint0__substrate__AraC" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="55"/>
-                      <layout:end layout:x="375" layout:y="90"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__AraC" layout:species="AraC">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="40"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI" layout:species="LacI">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="150"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__AraC__repression__LacI">
-            <layout:boundingBox>
-              <layout:position layout:x="110" layout:y="165"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__AraC__repression__LacI" layout:role="product" layout:speciesGlyph="Glyph__LacI">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="55"/>
-                      <layout:end layout:x="110" layout:y="165"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__LacI__repression__LacI">
-            <layout:boundingBox>
-              <layout:position layout:x="110" layout:y="165"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI__repression__LacI" layout:role="product" layout:speciesGlyph="Glyph__LacI">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="110" layout:y="165"/>
-                      <layout:end layout:x="110" layout:y="165"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__AraC__repression__AraC">
-            <layout:boundingBox>
-              <layout:position layout:x="70" layout:y="55"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__AraC__repression__AraC" layout:role="product" layout:speciesGlyph="Glyph__AraC">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="70" layout:y="55"/>
-                      <layout:end layout:x="70" layout:y="55"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__LacI__repression__AraC">
-            <layout:boundingBox>
-              <layout:position layout:x="70" layout:y="55"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI__repression__AraC" layout:role="product" layout:speciesGlyph="Glyph__AraC">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="110" layout:y="165"/>
-                      <layout:end layout:x="70" layout:y="55"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-        </layout:listOfReactionGlyphs>
-      </layout:layout>
-    </layout:listOfLayouts>
-    <listOfFunctionDefinitions>
-      <functionDefinition id="St" name="Steady State Property">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <apply>
-              <not/>
-              <apply>
-                <not/>
-                <ci> x </ci>
-              </apply>
-            </apply>
-          </lambda>
-        </math>
-            </functionDefinition>
-      <functionDefinition id="uniform" name="Uniform distribution">
-        <annotation>
-          <distribution xmlns="http://sbml.org/annotations/distribution" definition="http://en.wikipedia.org/wiki/Uniform_distribution_(continuous)"/>
-        </annotation>
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <bvar>
-              <ci> b </ci>
-            </bvar>
-            <apply>
-              <divide/>
-              <apply>
-                <plus/>
-                <ci> a </ci>
-                <ci> b </ci>
-              </apply>
-              <cn type="integer"> 2 </cn>
-            </apply>
-          </lambda>
-        </math>
-              <drawFromDistribution>
-          <listOfDistribInputs>
-            <distribInput distrib:id="a" distrib:index="0"/>
-            <distribInput distrib:id="b" distrib:index="1"/>
-          </listOfDistribInputs>
-          <UncertML xmlns="http://www.uncertml.org/3.0">
-            <UniformDistribution definition="http://www.uncertml.org/distributions">
-              <minimum>
-                <var varId="a"/>
-              </minimum>
-              <maximum>
-                <var varId="b"/>
-              </maximum>
-            </UniformDistribution>
-          </UncertML>
-        </drawFromDistribution>
-      </functionDefinition>
-      <functionDefinition id="PF" name="Probabilistic Eventually Property">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> t </ci>
-            </bvar>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <apply>
-              <ci> uniform </ci>
-              <cn type="integer"> 0 </cn>
-              <cn type="integer"> 1 </cn>
-            </apply>
-          </lambda>
-        </math>
-            </functionDefinition>
-    </listOfFunctionDefinitions>
-    <listOfUnitDefinitions/>
-    <listOfCompartments>
-      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="AraC" initialAmount="0" metaid="iBioSim24"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="LacI" initialAmount="0" metaid="iBioSim25"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P1" initialAmount="20" metaid="iBioSim26" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P2" initialAmount="20" metaid="iBioSim27" sboTerm="SBO:0000590"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="ko_r" metaid="iBioSim2" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="nr" metaid="iBioSim3" name="Initial RNAP count" value="100"/>
-      <parameter constant="true" id="np" metaid="iBioSim4" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="kr_r" metaid="iBioSim5" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="ka_f" metaid="iBioSim6" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="kecdiff" metaid="iBioSim7" name="Extracellular diffusion rate" value="1"/>
-      <parameter constant="true" id="ko" metaid="iBioSim8" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="kmdiff_f" metaid="iBioSim9" name="Forward membrane diffusion rate" value="1"/>
-      <parameter constant="true" id="kecd" metaid="iBioSim10" name="Extracellular degradation rate" value="0.005"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim11" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="kr_f" metaid="iBioSim12" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="ka_r" metaid="iBioSim13" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim14" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="kd" metaid="iBioSim15" name="Degradation rate" value="0.0075"/>
-      <parameter constant="true" id="kao_r" metaid="iBioSim16" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kb" metaid="iBioSim17" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="ng" metaid="iBioSim18" name="Initial promoter count" value="20"/>
-      <parameter constant="true" id="ka" metaid="iBioSim19" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="kao_f" metaid="iBioSim20" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kmdiff_r" metaid="iBioSim21" name="Reverse membrane diffusion rate" value="0.01"/>
-      <parameter constant="true" id="ko_f" metaid="iBioSim22" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim23" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="limit" metaid="iBioSim1" value="0"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="constraint0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <ci> St </ci>
-            <apply>
-              <or/>
-              <apply>
-                <and/>
-                <apply>
-                  <geq/>
-                  <ci> AraC </ci>
-                  <cn type="integer"> 60 </cn>
-                </apply>
-                <apply>
-                  <geq/>
-                  <apply>
-                    <ci> PF </ci>
-                    <apply>
-                      <leq/>
-                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-                      <cn type="integer"> 3000 </cn>
-                    </apply>
-                    <apply>
-                      <lt/>
-                      <ci> AraC </ci>
-                      <cn type="integer"> 60 </cn>
-                    </apply>
-                  </apply>
-                  <cn> 0.95 </cn>
-                </apply>
-              </apply>
-              <apply>
-                <and/>
-                <apply>
-                  <lt/>
-                  <ci> AraC </ci>
-                  <cn type="integer"> 60 </cn>
-                </apply>
-                <apply>
-                  <geq/>
-                  <apply>
-                    <ci> PF </ci>
-                    <apply>
-                      <leq/>
-                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-                      <cn type="integer"> 3000 </cn>
-                    </apply>
-                    <apply>
-                      <geq/>
-                      <ci> AraC </ci>
-                      <cn type="integer"> 60 </cn>
-                    </apply>
-                  </apply>
-                  <cn> 0.95 </cn>
-                </apply>
-              </apply>
-            </apply>
-          </apply>
-        </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="Degradation_AraC" metaid="iBioSim28" reversible="false" sboTerm="SBO:0000179">
-        <listOfReactants>
-          <speciesReference constant="true" species="AraC" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> AraC </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_LacI" metaid="iBioSim29" reversible="false" sboTerm="SBO:0000179">
-        <listOfReactants>
-          <speciesReference constant="true" species="LacI" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P1" metaid="iBioSim30" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="LacI" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
-          <modifierSpeciesReference sboTerm="SBO:0000459" species="AraC"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="LacI"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> P1 </ci>
-                <apply>
-                  <plus/>
-                  <apply>
-                    <times/>
-                    <ci> kb </ci>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                  <apply>
-                    <times/>
-                    <ci> ka </ci>
-                    <apply>
-                      <divide/>
-                      <ci> kao_f </ci>
-                      <ci> kao_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                    <apply>
-                      <power/>
-                      <apply>
-                        <times/>
-                        <apply>
-                          <divide/>
-                          <ci> ka_f </ci>
-                          <ci> ka_r </ci>
-                        </apply>
-                        <ci> AraC </ci>
-                      </apply>
-                      <ci> nc </ci>
-                    </apply>
-                  </apply>
-                </apply>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> kao_f </ci>
-                    <ci> kao_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                  <apply>
-                    <power/>
-                    <apply>
-                      <times/>
-                      <apply>
-                        <divide/>
-                        <ci> ka_f </ci>
-                        <ci> ka_r </ci>
-                      </apply>
-                      <ci> AraC </ci>
-                    </apply>
-                    <ci> nc </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> LacI </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P2" metaid="iBioSim31" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="AraC" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
-          <modifierSpeciesReference sboTerm="SBO:0000459" species="AraC"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="LacI"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> P2 </ci>
-                <apply>
-                  <plus/>
-                  <apply>
-                    <times/>
-                    <ci> kb </ci>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                  <apply>
-                    <times/>
-                    <ci> ka </ci>
-                    <apply>
-                      <divide/>
-                      <ci> kao_f </ci>
-                      <ci> kao_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                    <apply>
-                      <power/>
-                      <apply>
-                        <times/>
-                        <apply>
-                          <divide/>
-                          <ci> ka_f </ci>
-                          <ci> ka_r </ci>
-                        </apply>
-                        <ci> AraC </ci>
-                      </apply>
-                      <ci> nc </ci>
-                    </apply>
-                  </apply>
-                </apply>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> kao_f </ci>
-                    <ci> kao_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                  <apply>
-                    <power/>
-                    <apply>
-                      <times/>
-                      <apply>
-                        <divide/>
-                        <ci> ka_f </ci>
-                        <ci> ka_r </ci>
-                      </apply>
-                      <ci> AraC </ci>
-                    </apply>
-                    <ci> nc </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> LacI </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <listOfEvents/>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.props b/GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.props
new file mode 100644
index 0000000..7d417e3
--- /dev/null
+++ b/GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.props
@@ -0,0 +1 @@
+P=? [ true U[0,50] (AraC >= 2) ]
diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.sm b/GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.sm
similarity index 100%
rename from GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.sm
rename to GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.sm
diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.xml b/GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.xml
new file mode 100755
index 0000000..d2b7aba
--- /dev/null
+++ b/GeneticCircuits/Dual_Feedback_Osscillator/Dual_Feedback_Oscillator.xml
@@ -0,0 +1,400 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim32" id="dual_feedback_oscillator">
+    <addedPrefix:listOfFunctionDefinitions>
+      <addedPrefix:functionDefinition id="St" name="Steady State Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <not/>
+              <apply>
+                <not/>
+                <ci> x </ci>
+              </apply>
+            </apply>
+          </lambda>
+        </math>
+      </addedPrefix:functionDefinition>
+      <addedPrefix:functionDefinition id="uniform" name="Uniform distribution">
+        <annotation>
+          <distribution xmlns="http://sbml.org/annotations/distribution" definition="http://en.wikipedia.org/wiki/Uniform_distribution_(continuous)"/>
+        </annotation>
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> a </ci>
+            </bvar>
+            <bvar>
+              <ci> b </ci>
+            </bvar>
+            <apply>
+              <divide/>
+              <apply>
+                <plus/>
+                <ci> a </ci>
+                <ci> b </ci>
+              </apply>
+              <cn type="integer"> 2 </cn>
+            </apply>
+          </lambda>
+        </math>
+      </addedPrefix:functionDefinition>
+      <addedPrefix:functionDefinition id="PF" name="Probabilistic Eventually Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> t </ci>
+            </bvar>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <ci> uniform </ci>
+              <cn type="integer"> 0 </cn>
+              <cn type="integer"> 1 </cn>
+            </apply>
+          </lambda>
+        </math>
+      </addedPrefix:functionDefinition>
+    </addedPrefix:listOfFunctionDefinitions>
+    <addedPrefix:listOfCompartments>
+      <addedPrefix:compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
+    </addedPrefix:listOfCompartments>
+    <addedPrefix:listOfSpecies>
+      <addedPrefix:species metaid="iBioSim24" id="AraC" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim25" id="LacI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim26" id="P1" compartment="Cell" initialAmount="20" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim27" id="P2" compartment="Cell" initialAmount="20" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim2" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim3" id="nr" name="Initial RNAP count" value="100" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim4" id="np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim5" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim6" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim7" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim8" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim9" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim10" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim11" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim12" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim13" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim14" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim15" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim16" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim17" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim18" id="ng" name="Initial promoter count" value="20" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim19" id="ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim20" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim21" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim22" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim23" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim1" id="limit" value="0" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="constraint0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <ci> St </ci>
+            <apply>
+              <or/>
+              <apply>
+                <and/>
+                <apply>
+                  <geq/>
+                  <ci> AraC </ci>
+                  <cn type="integer"> 60 </cn>
+                </apply>
+                <apply>
+                  <geq/>
+                  <apply>
+                    <ci> PF </ci>
+                    <apply>
+                      <leq/>
+                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+                      <cn type="integer"> 3000 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <ci> AraC </ci>
+                      <cn type="integer"> 60 </cn>
+                    </apply>
+                  </apply>
+                  <cn> 0.95 </cn>
+                </apply>
+              </apply>
+              <apply>
+                <and/>
+                <apply>
+                  <lt/>
+                  <ci> AraC </ci>
+                  <cn type="integer"> 60 </cn>
+                </apply>
+                <apply>
+                  <geq/>
+                  <apply>
+                    <ci> PF </ci>
+                    <apply>
+                      <leq/>
+                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+                      <cn type="integer"> 3000 </cn>
+                    </apply>
+                    <apply>
+                      <geq/>
+                      <ci> AraC </ci>
+                      <cn type="integer"> 60 </cn>
+                    </apply>
+                  </apply>
+                  <cn> 0.95 </cn>
+                </apply>
+              </apply>
+            </apply>
+          </apply>
+        </math>
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim28" sboTerm="SBO:0000179" id="Degradation_AraC" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="AraC" stoichiometry="1"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> AraC </ci>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim29" sboTerm="SBO:0000179" id="Degradation_LacI" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="LacI" stoichiometry="1"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> LacI </ci>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim30" sboTerm="SBO:0000589" id="Production_P1" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="LacI" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000459" species="AraC"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="LacI"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> P1 </ci>
+                <apply>
+                  <plus/>
+                  <apply>
+                    <times/>
+                    <ci> kb </ci>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <times/>
+                    <ci> ka </ci>
+                    <apply>
+                      <divide/>
+                      <ci> kao_f </ci>
+                      <ci> kao_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                    <apply>
+                      <power/>
+                      <apply>
+                        <times/>
+                        <apply>
+                          <divide/>
+                          <ci> ka_f </ci>
+                          <ci> ka_r </ci>
+                        </apply>
+                        <ci> AraC </ci>
+                      </apply>
+                      <ci> nc </ci>
+                    </apply>
+                  </apply>
+                </apply>
+              </apply>
+              <apply>
+                <plus/>
+                <cn type="integer"> 1 </cn>
+                <apply>
+                  <times/>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                  <ci> nr </ci>
+                </apply>
+                <apply>
+                  <times/>
+                  <apply>
+                    <divide/>
+                    <ci> kao_f </ci>
+                    <ci> kao_r </ci>
+                  </apply>
+                  <ci> nr </ci>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <ci> ka_f </ci>
+                        <ci> ka_r </ci>
+                      </apply>
+                      <ci> AraC </ci>
+                    </apply>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> LacI </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim31" sboTerm="SBO:0000589" id="Production_P2" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="AraC" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000459" species="AraC"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="LacI"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> P2 </ci>
+                <apply>
+                  <plus/>
+                  <apply>
+                    <times/>
+                    <ci> kb </ci>
+                    <apply>
+                      <divide/>
+                      <ci> ko_f </ci>
+                      <ci> ko_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                  </apply>
+                  <apply>
+                    <times/>
+                    <ci> ka </ci>
+                    <apply>
+                      <divide/>
+                      <ci> kao_f </ci>
+                      <ci> kao_r </ci>
+                    </apply>
+                    <ci> nr </ci>
+                    <apply>
+                      <power/>
+                      <apply>
+                        <times/>
+                        <apply>
+                          <divide/>
+                          <ci> ka_f </ci>
+                          <ci> ka_r </ci>
+                        </apply>
+                        <ci> AraC </ci>
+                      </apply>
+                      <ci> nc </ci>
+                    </apply>
+                  </apply>
+                </apply>
+              </apply>
+              <apply>
+                <plus/>
+                <cn type="integer"> 1 </cn>
+                <apply>
+                  <times/>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                  <ci> nr </ci>
+                </apply>
+                <apply>
+                  <times/>
+                  <apply>
+                    <divide/>
+                    <ci> kao_f </ci>
+                    <ci> kao_r </ci>
+                  </apply>
+                  <ci> nr </ci>
+                  <apply>
+                    <power/>
+                    <apply>
+                      <times/>
+                      <apply>
+                        <divide/>
+                        <ci> ka_f </ci>
+                        <ci> ka_r </ci>
+                      </apply>
+                      <ci> AraC </ci>
+                    </apply>
+                    <ci> nc </ci>
+                  </apply>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> LacI </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
+</sbml>
diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/results.txt b/GeneticCircuits/Dual_Feedback_Osscillator/results.txt
new file mode 100644
index 0000000..8633f3b
--- /dev/null
+++ b/GeneticCircuits/Dual_Feedback_Osscillator/results.txt
@@ -0,0 +1,2 @@
+0.07166679484071543
+0.07166679514795181
diff --git a/GeneticCircuits/Muller_C_Element/Majority/Majority.props b/GeneticCircuits/Muller_C_Element/Majority/Majority.props
deleted file mode 100644
index c1cb805..0000000
--- a/GeneticCircuits/Muller_C_Element/Majority/Majority.props
+++ /dev/null
@@ -1,4 +0,0 @@
-//const int T;
-
-// Probability that the toggle switch changes state erroneously within T time units.
-"change_state" : P=? [ F<=2100 ((EE > 40) & (CC < 20))]
diff --git a/GeneticCircuits/Muller_C_Element/Majority/Majority.sm b/GeneticCircuits/Muller_C_Element/Majority/Majority.sm
deleted file mode 100644
index 7c8f04e..0000000
--- a/GeneticCircuits/Muller_C_Element/Majority/Majority.sm
+++ /dev/null
@@ -1,278 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: majority.xml
-
-ctmc
-
-const int MAX_AMOUNT = 200;
-
-// Compartment size
-const double default = 1.0;
-
-// Model parameters
-const double kr_f = 0.5; // kr_f
-const double kr_r = 1; // kr_r
-const double ka_f = 0.0033; // ka_f
-const double ka_r = 1; // ka_r
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double ko_f = 0.033; // ko_f
-const double ko_r = 1; // ko_r
-const double kao_f = 1; // kao_f
-const double kao_r = 1; // kao_r
-const double kmdiff_f = 1; // kmdiff_f
-const double kmdiff_r = 0.01; // kmdiff_r
-const double kd = 0.0075; // kd
-const double kecd = 0.005; // kecd
-const double nc = 2; // nc
-const double nr = 30; // nr
-const double ko = 0.05; // ko
-const double kb = 0.0001; // kb
-const double ng = 2; // ng
-const double np = 10; // np
-const double ka = 0.25; // ka
-const double kecdiff = 1; // kecdiff
-
-// Original Model did not have this module
-// Species AA
-const int AA_MAX = MAX_AMOUNT;
-module AA
-
-	AA : [0..AA_MAX] init 40; // Initial amount 0
-
-
-endmodule
-
-// Original Model did not have this module
-// Species B
-const int B_MAX = MAX_AMOUNT;
-module B
-
-	B : [0..B_MAX] init 120; // Initial amount 120
-
-
-endmodule
-
-// Species D
-const int D_MAX = MAX_AMOUNT;
-module D
-
-	D : [0..D_MAX] init 200; // Initial amount 200
-
-	// Degradation_D
-	[Degradation_D] D > 0 -> (D'=D-1);
-	// Production_P5
-	[Production_P5]  D <= D_MAX-10 -> (D'=D+10);
-	// Production_P4
-	[Production_P4]  D <= D_MAX-10 -> (D'=D+10);
-	// Production_P6
-	[Production_P6]  D <= D_MAX-10 -> (D'=D+10);
-
-endmodule
-
-// Species EE
-const int EE_MAX = MAX_AMOUNT;
-module EE
-
-	EE : [0..EE_MAX] init 0; // Initial amount 0
-
-	// Degradation_EE
-	[Degradation_EE] EE > 0 -> (EE'=EE-1);
-	// Production_P7
-	[Production_P7]  EE <= EE_MAX-10 -> (EE'=EE+10);
-
-endmodule
-
-// Species CC
-const int CC_MAX = MAX_AMOUNT;
-module CC
-
-	CC : [0..CC_MAX] init 120; // Initial amount 120
-
-	// Degradation_CC
-	[Degradation_CC] CC > 0 -> (CC'=CC-1);
-	// Production_P8
-	[Production_P8]  CC <= CC_MAX-10 -> (CC'=CC+10);
-
-endmodule
-
-// Species Y
-const int Y_MAX = MAX_AMOUNT;
-module Y
-
-	Y : [0..Y_MAX] init 0; // Initial amount 0
-
-	// Degradation_Y
-	[Degradation_Y] Y > 0 -> (Y'=Y-1);
-	// Production_P1
-	[Production_P1]  Y <= Y_MAX-10 -> (Y'=Y+10);
-	// Production_P3
-	[Production_P3]  Y <= Y_MAX-10 -> (Y'=Y+10);
-
-endmodule
-
-// Species XX
-const int XX_MAX = MAX_AMOUNT;
-module XX
-
-	XX : [0..XX_MAX] init 0; // Initial amount 0
-
-	// Degradation_XX
-	[Degradation_XX] XX > 0 -> (XX'=XX-1);
-	// Production_P1
-	[Production_P1]  XX <= XX_MAX-10 -> (XX'=XX+10);
-	// Production_P2
-	[Production_P2]  XX <= XX_MAX-10 -> (XX'=XX+10);
-
-endmodule
-
-// Species Z
-const int Z_MAX = MAX_AMOUNT;
-module Z
-
-	Z : [0..Z_MAX] init 0; // Initial amount 0
-
-	// Degradation_Z
-	[Degradation_Z] Z > 0 -> (Z'=Z-1);
-	// Production_P3
-	[Production_P3]  Z <= Z_MAX-10 -> (Z'=Z+10);
-	// Production_P2
-	[Production_P2]  Z <= Z_MAX-10 -> (Z'=Z+10);
-
-endmodule
-
-// Species P8 (P8)
-const int P8_MAX = MAX_AMOUNT;
-module P8
-
-	P8 : [0..P8_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P5 (P5)
-const int P5_MAX = MAX_AMOUNT;
-module P5
-
-	P5 : [0..P5_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P4 (P4)
-const int P4_MAX = MAX_AMOUNT;
-module P4
-
-	P4 : [0..P4_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P7 (P7)
-const int P7_MAX = MAX_AMOUNT;
-module P7
-
-	P7 : [0..P7_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P6 (P6)
-const int P6_MAX = MAX_AMOUNT;
-module P6
-
-	P6 : [0..P6_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P1 (P1)
-const int P1_MAX = MAX_AMOUNT;
-module P1
-
-	P1 : [0..P1_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P3 (P3)
-const int P3_MAX = MAX_AMOUNT;
-module P3
-
-	P3 : [0..P3_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P2 (P2)
-const int P2_MAX = MAX_AMOUNT;
-module P2
-
-	P2 : [0..P2_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// Degradation_D: D ->
-	[Degradation_D] (kd*D) > 0 -> (kd*D) : true;
-	// Degradation_EE: EE ->
-	[Degradation_EE] (kd*EE) > 0 -> (kd*EE) : true;
-	// Degradation_CC: CC ->
-	[Degradation_CC] (kd*CC) > 0 -> (kd*CC) : true;
-	// Degradation_Y: Y ->
-	[Degradation_Y] (kd*Y) > 0 -> (kd*Y) : true;
-	// Degradation_XX: XX ->
-	[Degradation_XX] (kd*XX) > 0 -> (kd*XX) : true;
-	// Degradation_Z: Z ->
-	[Degradation_Z] (kd*Z) > 0 -> (kd*Z) : true;
-	// Production_P8:  -> CC
-	[Production_P8] ((((P8*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*EE),nc)))) > 0 -> ((((P8*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*EE),nc)))) : true;
-	// Production_P5:  -> D
-	[Production_P5] ((((P5*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Y),nc)))) > 0 -> ((((P5*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Y),nc)))) : true;
-	// Production_P4:  -> D
-	[Production_P4] ((((P4*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*XX),nc)))) > 0 -> ((((P4*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*XX),nc)))) : true;
-	// Production_P7:  -> EE
-	[Production_P7] ((((P7*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) > 0 -> ((((P7*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) : true;
-	// Production_P6:  -> D
-	[Production_P6] ((((P6*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Z),nc)))) > 0 -> ((((P6*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*Z),nc)))) : true;
-	// Production_P1:  -> Y+XX
-	[Production_P1] ((((P1*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*AA),nc)))) > 0 -> ((((P1*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*AA),nc)))) : true;
-	// Production_P3:  -> Z+Y
-	[Production_P3] ((((P3*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) > 0 -> ((((P3*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*D),nc)))) : true;
-	// Production_P2:  -> XX+Z
-	[Production_P2] ((((P2*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*B),nc)))) > 0 -> ((((P2*ko*ko_f)/ko_r)*nr)/(1+((ko_f/ko_r)*nr)+(func(pow,((kr_f/kr_r)*B),nc)))) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: D
-rewards "D" true : D; endrewards
-// Reward 2: EE
-rewards "EE" true : EE; endrewards
-// Reward 5: CC
-rewards "CC" true : CC; endrewards
-// Reward 6: Y
-rewards "Y" true : Y; endrewards
-// Reward 7: XX
-rewards "XX" true : XX; endrewards
-// Reward 8: Z
-rewards "Z" true : Z; endrewards
-// Reward 9: P8 (P8)
-rewards "P8" true : P8; endrewards
-// Reward 10: P5 (P5)
-rewards "P5" true : P5; endrewards
-// Reward 11: P4 (P4)
-rewards "P4" true : P4; endrewards
-// Reward 12: P7 (P7)
-rewards "P7" true : P7; endrewards
-// Reward 13: P6 (P6)
-rewards "P6" true : P6; endrewards
-// Reward 14: P1 (P1)
-rewards "P1" true : P1; endrewards
-// Reward 15: P3 (P3)
-rewards "P3" true : P3; endrewards
-// Reward 16: P2 (P2)
-rewards "P2" true : P2; endrewards
diff --git a/GeneticCircuits/Muller_C_Element/Majority/Majority.xml b/GeneticCircuits/Muller_C_Element/Majority/Majority.xml
deleted file mode 100755
index 7620cb9..0000000
--- a/GeneticCircuits/Muller_C_Element/Majority/Majority.xml
+++ /dev/null
@@ -1,1228 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="2" version="2" layout:required="false" comp:required="true" fbc:required="false" arrays:required="true">
-  <model metaid="iBioSim58" id="majority" name="Created from majority.gcm" substanceUnits="mole" volumeUnits="litre">
-    <listOfFunctionDefinitions>
-      <functionDefinition id="neighborQuantityLeft" name="neighborQuantityLeft">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="neighborQuantityRight" name="neighborQuantityRight">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="neighborQuantityAbove" name="neighborQuantityAbove">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="neighborQuantityBelow" name="neighborQuantityBelow">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="getCompartmentLocationX" name="getCompartmentLocationX">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="getCompartmentLocationY" name="getCompartmentLocationY">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="F" name="Eventually Property">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> t </ci>
-            </bvar>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <apply>
-              <or/>
-              <apply>
-                <not/>
-                <ci> t </ci>
-              </apply>
-              <apply>
-                <not/>
-                <ci> x </ci>
-              </apply>
-            </apply>
-          </lambda>
-        </math>
-      </functionDefinition>
-    </listOfFunctionDefinitions>
-    <listOfCompartments>
-      <compartment id="default" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species metaid="iBioSim2" id="D" compartment="default" initialAmount="200" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim3" id="EE" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim4" id="AA" compartment="default" initialAmount="40" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
-      <species metaid="iBioSim5" id="B" compartment="default" initialAmount="120" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
-      <species metaid="iBioSim6" id="CC" compartment="default" initialAmount="120" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim7" id="Y" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim8" id="XX" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim9" id="Z" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim10" sboTerm="SBO:0000590" id="P8" name="P8" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim11" sboTerm="SBO:0000590" id="P5" name="P5" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim12" sboTerm="SBO:0000590" id="P4" name="P4" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim13" sboTerm="SBO:0000590" id="P7" name="P7" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim14" sboTerm="SBO:0000590" id="P6" name="P6" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim15" sboTerm="SBO:0000590" id="P1" name="P1" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim16" sboTerm="SBO:0000590" id="P3" name="P3" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim17" sboTerm="SBO:0000590" id="P2" name="P2" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter metaid="iBioSim18" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
-      <parameter metaid="iBioSim19" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim20" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
-      <parameter metaid="iBioSim21" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim22" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
-      <parameter metaid="iBioSim23" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim24" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
-      <parameter metaid="iBioSim25" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim26" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim27" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim28" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim29" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
-      <parameter metaid="iBioSim30" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
-      <parameter metaid="iBioSim31" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
-      <parameter metaid="iBioSim32" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
-      <parameter metaid="iBioSim33" id="nr" name="Initial RNAP count" value="30" constant="true"/>
-      <parameter metaid="iBioSim34" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
-      <parameter metaid="iBioSim35" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
-      <parameter metaid="iBioSim36" id="ng" name="Initial promoter count" value="2" constant="true"/>
-      <parameter metaid="iBioSim37" id="np" name="Stoichiometry of production" value="10" constant="true"/>
-      <parameter metaid="iBioSim38" id="ka" name="Activated production rate" value="0.25" constant="true"/>
-      <parameter metaid="iBioSim39" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="Condition_0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <ci> F </ci>
-            <apply>
-              <leq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 2100 </cn>
-            </apply>
-            <apply>
-              <and/>
-              <apply>
-                <gt/>
-                <ci> EE </ci>
-                <cn type="integer"> 40 </cn>
-              </apply>
-              <apply>
-                <lt/>
-                <ci> CC </ci>
-                <cn type="integer"> 20 </cn>
-              </apply>
-            </apply>
-          </apply>
-        </math>
-        <message>
-          <p xmlns="http://www.w3.org/1999/xhtml">Pr=?{(true)PU[0,2100]((E greater than 40) and (C less than 20))}</p>
-        </message>
-      </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction metaid="iBioSim40" sboTerm="SBO:0000179" id="Degradation_D" reversible="false" compartment="default">
-        <listOfReactants>
-          <speciesReference species="D" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> D </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim41" sboTerm="SBO:0000179" id="Degradation_EE" reversible="false" compartment="default">
-        <listOfReactants>
-          <speciesReference species="EE" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> EE </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim44" sboTerm="SBO:0000179" id="Degradation_CC" reversible="false" compartment="default">
-        <listOfReactants>
-          <speciesReference species="CC" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> CC </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim45" sboTerm="SBO:0000179" id="Degradation_Y" reversible="false" compartment="default">
-        <listOfReactants>
-          <speciesReference species="Y" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Y </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim46" sboTerm="SBO:0000179" id="Degradation_XX" reversible="false" compartment="default">
-        <listOfReactants>
-          <speciesReference species="XX" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> XX </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim47" sboTerm="SBO:0000179" id="Degradation_Z" reversible="false" compartment="default">
-        <listOfReactants>
-          <speciesReference species="Z" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Z </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim48" sboTerm="SBO:0000589" id="Production_P8" reversible="false" compartment="default">
-        <listOfProducts>
-          <speciesReference species="CC" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="EE"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <ci> P8 </ci>
-                    <ci> ko </ci>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> EE </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim49" sboTerm="SBO:0000589" id="Production_P5" reversible="false" compartment="default">
-        <listOfProducts>
-          <speciesReference species="D" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <ci> P5 </ci>
-                    <ci> ko </ci>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> Y </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim50" sboTerm="SBO:0000589" id="Production_P4" reversible="false" compartment="default">
-        <listOfProducts>
-          <speciesReference species="D" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="XX"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <ci> P4 </ci>
-                    <ci> ko </ci>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> XX </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim51" sboTerm="SBO:0000589" id="Production_P7" reversible="false" compartment="default">
-        <listOfProducts>
-          <speciesReference species="EE" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <ci> P7 </ci>
-                    <ci> ko </ci>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> D </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim52" sboTerm="SBO:0000589" id="Production_P6" reversible="false" compartment="default">
-        <listOfProducts>
-          <speciesReference species="D" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <ci> P6 </ci>
-                    <ci> ko </ci>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> Z </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim53" sboTerm="SBO:0000589" id="Production_P1" reversible="false" compartment="default">
-        <listOfProducts>
-          <speciesReference species="Y" stoichiometry="10" constant="true"/>
-          <speciesReference species="XX" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="AA"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <ci> P1 </ci>
-                    <ci> ko </ci>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
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-                  <ci> nr </ci>
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-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
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-                    <ci> AA </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim54" sboTerm="SBO:0000589" id="Production_P3" reversible="false" compartment="default">
-        <listOfProducts>
-          <speciesReference species="Z" stoichiometry="10" constant="true"/>
-          <speciesReference species="Y" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <ci> P3 </ci>
-                    <ci> ko </ci>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
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diff --git a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props
index bc22858..7813f8a 100644
--- a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props
+++ b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.props
@@ -1,4 +1,6 @@
 //const int T;
 
 // Probability that the toggle switch changes state erroneously within T time units.
-"change_state" : P=? [ F<=2100 ((_E > 40) & (_C < 20))]
+//"change_state" : P=? [ F<=2100 ((_E > 40) & (_C < 20))]
+
+P=? [ true U[0,50] (_C <= 65) ]
diff --git a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml
index cc64d57..20f20b8 100644
--- a/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml
+++ b/GeneticCircuits/Muller_C_Element/Majority_10_10/Majority_10_10.xml
@@ -1,754 +1,8 @@
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-      <comp:port comp:id="output__C" comp:idRef="C" sboTerm="SBO:0000601"/>
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@@ -770,49 +24,49 @@
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-    <listOfCompartments>
-      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="A" initialAmount="0" metaid="iBioSim1"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="X" initialAmount="70" metaid="iBioSim3"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Y" initialAmount="70" metaid="iBioSim5"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="D" initialAmount="70" metaid="iBioSim6"/>
-      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="B" initialAmount="120" metaid="iBioSim7"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Z" initialAmount="0" metaid="iBioSim8"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="E" initialAmount="0" metaid="iBioSim9"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="C" initialAmount="70" metaid="iBioSim10"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P8" initialAmount="2" metaid="iBioSim11" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P1" initialAmount="2" metaid="iBioSim13" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P2" initialAmount="2" metaid="iBioSim15" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P3" initialAmount="2" metaid="iBioSim17" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P4" initialAmount="2" metaid="iBioSim19" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P5" initialAmount="2" metaid="iBioSim21" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P6" initialAmount="2" metaid="iBioSim23" sboTerm="SBO:0000590"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P7" initialAmount="2" metaid="iBioSim25" sboTerm="SBO:0000590"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kr_f" metaid="iBioSim4" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="kr_r" metaid="iBioSim12" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="ka_f" metaid="iBioSim27" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="ka_r" metaid="iBioSim29" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="ko_f" metaid="iBioSim30" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="ko_r" metaid="iBioSim31" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kao_f" metaid="iBioSim32" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kao_r" metaid="iBioSim33" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim34" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="nr" metaid="iBioSim35" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="ko" metaid="iBioSim36" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="kb" metaid="iBioSim37" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="ng" metaid="iBioSim38" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="np" metaid="iBioSim39" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="ka" metaid="iBioSim40" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="kd" metaid="iBioSim2" name="Degradation rate" value="0.00075"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:functionDefinition>
+    </addedPrefix:listOfFunctionDefinitions>
+    <addedPrefix:listOfCompartments>
+      <addedPrefix:compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
+    </addedPrefix:listOfCompartments>
+    <addedPrefix:listOfSpecies>
+      <addedPrefix:species metaid="iBioSim1" id="A" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
+      <addedPrefix:species metaid="iBioSim3" id="X" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim5" id="Y" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim6" id="D" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim7" id="B" compartment="Cell" initialAmount="120" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
+      <addedPrefix:species metaid="iBioSim8" id="Z" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim9" id="E" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim10" id="C" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim11" id="P8" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim13" id="P1" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim15" id="P2" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim17" id="P3" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim19" id="P4" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim21" id="P5" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim23" id="P6" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim25" id="P7" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim4" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim12" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim27" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim29" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim30" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim31" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim32" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim33" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim34" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim35" id="nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim36" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim37" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim38" id="ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim39" id="np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim40" id="ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim2" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <ci> F </ci>
@@ -836,14 +90,14 @@
             </apply>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="Degradation_C" metaid="iBioSim46" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="C" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim46" id="Degradation_C" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="C" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -851,13 +105,13 @@
               <ci> C </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_D" metaid="iBioSim44" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="D" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim44" id="Degradation_D" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="D" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -865,13 +119,13 @@
               <ci> D </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_E" metaid="iBioSim45" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="E" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim45" id="Degradation_E" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="E" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -879,13 +133,13 @@
               <ci> E </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_X" metaid="iBioSim47" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim47" id="Degradation_X" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -893,13 +147,13 @@
               <ci> X </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_Y" metaid="iBioSim43" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim43" id="Degradation_Y" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -907,13 +161,13 @@
               <ci> Y </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_Z" metaid="iBioSim42" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim42" id="Degradation_Z" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -921,18 +175,18 @@
               <ci> Z </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P1" metaid="iBioSim14" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim14" sboTerm="SBO:0000589" id="Production_P1" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -942,11 +196,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P1 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P1 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -955,18 +206,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -984,18 +232,18 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P2" metaid="iBioSim16" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim16" sboTerm="SBO:0000589" id="Production_P2" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1005,11 +253,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P2 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P2 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1018,18 +263,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1047,52 +289,43 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P3" metaid="iBioSim18" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim18" sboTerm="SBO:0000589" id="Production_P3" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P3 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P3 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1110,17 +343,17 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P4" metaid="iBioSim20" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="D" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim20" sboTerm="SBO:0000589" id="Production_P4" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="D" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1130,11 +363,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P4 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P4 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1143,18 +373,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1172,17 +399,17 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P5" metaid="iBioSim22" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="D" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim22" sboTerm="SBO:0000589" id="Production_P5" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="D" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1192,11 +419,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P5 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P5 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1205,18 +429,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1234,51 +455,42 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P6" metaid="iBioSim24" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="D" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim24" sboTerm="SBO:0000589" id="Production_P6" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="D" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P6 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P6 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1296,17 +508,17 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P7" metaid="iBioSim26" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="E" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim26" sboTerm="SBO:0000589" id="Production_P7" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="E" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1316,11 +528,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P7 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P7 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1329,18 +538,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1358,51 +564,42 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P8" metaid="iBioSim28" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="C" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="E"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim28" sboTerm="SBO:0000589" id="Production_P8" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="C" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="E"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P8 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P8 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1420,8 +617,8 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Muller_C_Element/Majority_10_10/results.txt b/GeneticCircuits/Muller_C_Element/Majority_10_10/results.txt
new file mode 100644
index 0000000..5d4220f
--- /dev/null
+++ b/GeneticCircuits/Muller_C_Element/Majority_10_10/results.txt
@@ -0,0 +1,2 @@
+0.6954372359336837
+0.6954373474398886
diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.props b/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.props
deleted file mode 100644
index ef52047..0000000
--- a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.props
+++ /dev/null
@@ -1,2 +0,0 @@
-// Probability that the toggle switch changes state erroneously within T time units.
-"change_state" : P=? [ F<=2100 ((S2 > 80) & (S3 < 20))]
diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.sm b/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.sm
deleted file mode 100644
index 5d518b1..0000000
--- a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.sm
+++ /dev/null
@@ -1,343 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: speedInd.xml
-
-ctmc
-
-const int MAX_AMOUNT = 200;
-
-// Compartment size
-const double default = 1.0;
-
-
-// Model parameters
-const double kr_f = 0.5; // kr_f
-const double kr_r = 1; // kr_r
-const double ka_f = 0.0033; // ka_f
-const double ka_r = 1; // ka_r
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double ko_f = 0.033; // ko_f
-const double ko_r = 1; // ko_r
-const double kao_f = 1; // kao_f
-const double kao_r = 1; // kao_r
-const double kmdiff_f = 1; // kmdiff_f
-const double kmdiff_r = 0.01; // kmdiff_r
-const double kd = 0.0075; // kd
-const double kecd = 0.005; // kecd
-const double nc = 2; // nc
-const double nr = 30; // nr
-const double ko = 0.05; // ko
-const double kb = 0.0001; // kb
-const double ng = 2; // ng
-const double np = 10; // np
-const double ka = 0.25; // ka
-const double kecdiff = 1; // kecdiff
-
-// Species AA
-const int AA_MAX = MAX_AMOUNT;
-module AA
-
-	AA : [0..AA_MAX] init 0; // Initial amount 0
-
-
-endmodule
-
-// Species B
-const int B_MAX = MAX_AMOUNT;
-module B
-
-	B : [0..B_MAX] init 120; // Initial amount 120
-
-
-endmodule
-
-// Species CC
-const int CC_MAX = MAX_AMOUNT;
-module CC
-
-	CC : [0..CC_MAX] init 120; // Initial amount 120
-
-	// Degradation_CC
-	[Degradation_CC] CC > 0 -> (CC'=CC-1);
-	// Production_P9
-	[Production_P9]  CC <= CC_MAX-10 -> (CC'=CC+10);
-
-endmodule
-
-// Species S1
-const int S1_MAX = MAX_AMOUNT;
-module S1
-
-	S1 : [0..S1_MAX] init 200; // Initial amount 200
-
-	// Degradation_S1
-	[Degradation_S1] S1 > 0 -> (S1'=S1-1);
-	// Production_P4
-	[Production_P4]  S1 <= S1_MAX-10 -> (S1'=S1+10);
-	// Production_P7
-	[Production_P7]  S1 <= S1_MAX-10 -> (S1'=S1+10);
-
-endmodule
-
-// Species S2
-const int S2_MAX = MAX_AMOUNT;
-module S2
-
-	S2 : [0..S2_MAX] init 0; // Initial amount 0
-
-	// Degradation_S2
-	[Degradation_S2] S2 > 0 -> (S2'=S2-1);
-	// Production_P8
-	[Production_P8]  S2 <= S2_MAX-10 -> (S2'=S2+10);
-	// Production_P5
-	[Production_P5]  S2 <= S2_MAX-10 -> (S2'=S2+10);
-
-endmodule
-
-// Species S3
-const int S3_MAX = MAX_AMOUNT;
-module S3
-
-	S3 : [0..S3_MAX] init 120; // Initial amount 120
-
-	// Degradation_S3
-	[Degradation_S3] S3 > 0 -> (S3'=S3-1);
-	// Production_P6
-	[Production_P6]  S3 <= S3_MAX-10 -> (S3'=S3+10);
-	// Production_P3
-	[Production_P3]  S3 <= S3_MAX-10 -> (S3'=S3+10);
-
-endmodule
-
-// Species S4
-const int S4_MAX = MAX_AMOUNT;
-module S4
-
-	S4 : [0..S4_MAX] init 0; // Initial amount 0
-
-	// Degradation_S4
-	[Degradation_S4] S4 > 0 -> (S4'=S4-1);
-	// Production_P1
-	[Production_P1]  S4 <= S4_MAX-10 -> (S4'=S4+10);
-	// Production_P2
-	[Production_P2]  S4 <= S4_MAX-10 -> (S4'=S4+10);
-	// Production_P10
-	[Production_P10]  S4 <= S4_MAX-10 -> (S4'=S4+10);
-
-endmodule
-
-// Species XX
-const int XX_MAX = MAX_AMOUNT;
-module XX
-
-	XX : [0..XX_MAX] init 0; // Initial amount 0
-
-	// Degradation_XX
-	[Degradation_XX] XX > 0 -> (XX'=XX-1);
-	// Production_P1
-	[Production_P1]  XX <= XX_MAX-10 -> (XX'=XX+10);
-
-endmodule
-
-// Species Y
-const int Y_MAX = MAX_AMOUNT;
-module Y
-
-	Y : [0..Y_MAX] init 0; // Initial amount 0
-
-	// Degradation_Y
-	[Degradation_Y] Y > 0 -> (Y'=Y-1);
-	// Production_P2
-	[Production_P2]  Y <= Y_MAX-10 -> (Y'=Y+10);
-
-endmodule
-
-// Species Z
-const int Z_MAX = MAX_AMOUNT;
-module Z
-
-	Z : [0..Z_MAX] init 0; // Initial amount 0
-
-	// Degradation_Z
-	[Degradation_Z] Z > 0 -> (Z'=Z-1);
-	// Production_P8
-	[Production_P8]  Z <= Z_MAX-10 -> (Z'=Z+10);
-	// Production_P3
-	[Production_P3]  Z <= Z_MAX-10 -> (Z'=Z+10);
-
-endmodule
-
-// Species P9
-const int P9_MAX = MAX_AMOUNT;
-module P9
-
-	P9 : [0..P9_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P8
-const int P8_MAX = MAX_AMOUNT;
-module P8
-
-	P8 : [0..P8_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P5
-const int P5_MAX = MAX_AMOUNT;
-module P5
-
-	P5 : [0..P5_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P4
-const int P4_MAX = MAX_AMOUNT;
-module P4
-
-	P4 : [0..P4_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P7
-const int P7_MAX = MAX_AMOUNT;
-module P7
-
-	P7 : [0..P7_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P6
-const int P6_MAX = MAX_AMOUNT;
-module P6
-
-	P6 : [0..P6_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P1
-const int P1_MAX = MAX_AMOUNT;
-module P1
-
-	P1 : [0..P1_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P3
-const int P3_MAX = MAX_AMOUNT;
-module P3
-
-	P3 : [0..P3_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P2
-const int P2_MAX = MAX_AMOUNT;
-module P2
-
-	P2 : [0..P2_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Species P10
-const int P10_MAX = MAX_AMOUNT;
-module P10
-
-	P10 : [0..P10_MAX] init 2; // Initial amount 2
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// Degradation_S3: S3 ->
-	[Degradation_S3] (kd*S3) > 0 -> (kd*S3) : true;
-	// Degradation_S4: S4 ->
-	[Degradation_S4] (kd*S4) > 0 -> (kd*S4) : true;
-	// Degradation_CC: CC ->
-	[Degradation_CC] (kd*CC) > 0 -> (kd*CC) : true;
-	// Degradation_S2: S2 ->
-	[Degradation_S2] (kd*S2) > 0 -> (kd*S2) : true;
-	// Degradation_S1: S1 ->
-	[Degradation_S1] (kd*S1) > 0 -> (kd*S1) : true;
-	// Degradation_Y: Y ->
-	[Degradation_Y] (kd*Y) > 0 -> (kd*Y) : true;
-	// Degradation_XX: XX ->
-	[Degradation_XX] (kd*XX) > 0 -> (kd*XX) : true;
-	// Degradation_Z: Z ->
-	[Degradation_Z] (kd*Z) > 0 -> (kd*Z) : true;
-	// Production_P9:  -> CC
-	[Production_P9] (((((P9*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) > 0 -> (((((P9*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) : true;
-	// Production_P8:  -> Z+S2
-	[Production_P8] (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S3),nc)))) > 0 -> (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S3),nc)))) : true;
-	// Production_P5:  -> S2
-	[Production_P5] (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S1),nc)))) > 0 -> (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S1),nc)))) : true;
-	// Production_P4:  -> S1
-	[Production_P4] (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) > 0 -> (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) : true;
-	// Production_P7:  -> S1
-	[Production_P7] (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) > 0 -> (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) : true;
-	// Production_P6:  -> S3
-	[Production_P6] (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) > 0 -> (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) : true;
-	// Production_P1:  -> S4+XX
-	[Production_P1] (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) > 0 -> (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) : true;
-	// Production_P3:  -> S3+Z
-	[Production_P3] (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S4),nc)))) > 0 -> (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S4),nc)))) : true;
-	// Production_P2:  -> S4+Y
-	[Production_P2] (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) > 0 -> (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) : true;
-	// Production_P10:  -> S4
-	[Production_P10] (((((P10*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) > 0 -> (((((P10*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*S2),nc)))) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: AA
-rewards "AA" true : AA; endrewards
-// Reward 2: B
-rewards "B" true : B; endrewards
-// Reward 3: CC
-rewards "CC" true : CC; endrewards
-// Reward 4: S1
-rewards "S1" true : S1; endrewards
-// Reward 5: S2
-rewards "S2" true : S2; endrewards
-// Reward 6: S3
-rewards "S3" true : S3; endrewards
-// Reward 7: S4
-rewards "S4" true : S4; endrewards
-// Reward 8: XX
-rewards "XX" true : XX; endrewards
-// Reward 9: Y
-rewards "Y" true : Y; endrewards
-// Reward 10: Z
-rewards "Z" true : Z; endrewards
-// Reward 11: P9
-rewards "P9" true : P9; endrewards
-// Reward 12: P8
-rewards "P8" true : P8; endrewards
-// Reward 13: P5
-rewards "P5" true : P5; endrewards
-// Reward 14: P4
-rewards "P4" true : P4; endrewards
-// Reward 15: P7
-rewards "P7" true : P7; endrewards
-// Reward 16: P6
-rewards "P6" true : P6; endrewards
-// Reward 17: P1
-rewards "P1" true : P1; endrewards
-// Reward 18: P3
-rewards "P3" true : P3; endrewards
-// Reward 19: P2
-rewards "P2" true : P2; endrewards
-// Reward 20: P10
-rewards "P10" true : P10; endrewards
diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.xml b/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.xml
deleted file mode 100755
index 2227d47..0000000
--- a/GeneticCircuits/Muller_C_Element/Speed_Independent/Speed_Independent.xml
+++ /dev/null
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-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__B__repression__Y" layout:role="product" layout:speciesGlyph="Glyph__Y">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
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-          <layout:reactionGlyph layout:id="Glyph__S2__repression__S4">
-            <layout:boundingBox>
-              <layout:position layout:x="330" layout:y="384.82799358403304"/>
-              <layout:dimensions layout:width="0" layout:height="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__S2__repression__S4" layout:role="product" layout:speciesGlyph="Glyph__S4">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="368.309886183791" layout:y="15"/>
-                      <layout:end layout:x="330" layout:y="384.82799358403304"/>
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-                </layout:curve>
-              </layout:speciesReferenceGlyph>
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-          </layout:reactionGlyph>
-        </layout:listOfReactionGlyphs>
-        <layout:listOfTextGlyphs>
-          <layout:textGlyph layout:graphicalObject="Glyph__AA" layout:id="TextGlyph__AA" layout:text="AA">
-            <layout:boundingBox>
-              <layout:position layout:x="10" layout:y="379.673050492137"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__S3" layout:id="TextGlyph__S3" layout:text="S3">
-            <layout:boundingBox>
-              <layout:position layout:x="720" layout:y="359.61977236758105"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__S4" layout:id="TextGlyph__S4" layout:text="S4">
-            <layout:boundingBox>
-              <layout:position layout:x="280" layout:y="369.82799358403304"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__XX" layout:id="TextGlyph__XX" layout:text="XX">
-            <layout:boundingBox>
-              <layout:position layout:x="40" layout:y="329.673050492137"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__Z" layout:id="TextGlyph__Z" layout:text="Z">
-            <layout:boundingBox>
-              <layout:position layout:x="500" layout:y="369.82799358403304"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-        </layout:listOfTextGlyphs>
-      </layout:layout>
-    </layout:listOfLayouts>
-    <listOfFunctionDefinitions>
-      <functionDefinition id="neighborQuantityLeft" name="neighborQuantityLeft">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-            </functionDefinition>
-      <functionDefinition id="neighborQuantityRight" name="neighborQuantityRight">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-            </functionDefinition>
-      <functionDefinition id="neighborQuantityAbove" name="neighborQuantityAbove">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-            </functionDefinition>
-      <functionDefinition id="neighborQuantityBelow" name="neighborQuantityBelow">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-            </functionDefinition>
-      <functionDefinition id="getCompartmentLocationX" name="getCompartmentLocationX">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-            </functionDefinition>
-      <functionDefinition id="getCompartmentLocationY" name="getCompartmentLocationY">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> a </ci>
-            </bvar>
-            <cn type="integer"> 0 </cn>
-          </lambda>
-        </math>
-            </functionDefinition>
-      <functionDefinition id="F" name="Eventually Property">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> t </ci>
-            </bvar>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <apply>
-              <or/>
-              <apply>
-                <not/>
-                <ci> t </ci>
-              </apply>
-              <apply>
-                <not/>
-                <ci> x </ci>
-              </apply>
-            </apply>
-          </lambda>
-        </math>
-            </functionDefinition>
-    </listOfFunctionDefinitions>
-    <listOfCompartments>
-      <compartment id="default" constant="true" spatialDimensions="3" size="1"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species id="AA" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim2" boundaryCondition="false" compartment="default"/>
-      <species id="B" constant="false" initialAmount="120" hasOnlySubstanceUnits="true" metaid="iBioSim3" boundaryCondition="false" compartment="default"/>
-      <species id="CC" constant="false" initialAmount="120" hasOnlySubstanceUnits="true" metaid="iBioSim4" boundaryCondition="false" compartment="default"/>
-      <species id="S1" constant="false" initialAmount="200" hasOnlySubstanceUnits="true" metaid="iBioSim5" boundaryCondition="false" compartment="default"/>
-      <species id="S2" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim6" boundaryCondition="false" compartment="default"/>
-      <species id="S3" constant="false" initialAmount="120" hasOnlySubstanceUnits="true" metaid="iBioSim7" boundaryCondition="false" compartment="default"/>
-      <species id="S4" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim8" boundaryCondition="false" compartment="default"/>
-      <species id="XX" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim9" boundaryCondition="false" compartment="default"/>
-      <species id="Y" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim10" boundaryCondition="false" compartment="default"/>
-      <species id="Z" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim11" boundaryCondition="false" compartment="default"/>
-      <species id="P9" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim34" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P8" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim35" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P5" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim36" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P4" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim37" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P7" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim38" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P6" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim39" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P1" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim40" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P3" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim41" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P2" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim42" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P10" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim43" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="kr_f" constant="true" name="Forward repression binding rate" metaid="iBioSim12" value="0.5"/>
-      <parameter id="kr_r" constant="true" name="Reverse repression binding rate" metaid="iBioSim13" value="1"/>
-      <parameter id="ka_f" constant="true" name="Forward activation binding rate" metaid="iBioSim14" value="0.0033"/>
-      <parameter id="ka_r" constant="true" name="Reverse activation binding rate" metaid="iBioSim15" value="1"/>
-      <parameter id="kc_f" constant="true" name="Forward complex formation rate" metaid="iBioSim16" value="0.05"/>
-      <parameter id="kc_r" constant="true" name="Reverse complex formation rate" metaid="iBioSim17" value="1"/>
-      <parameter id="ko_f" constant="true" name="Forward RNAP binding rate" metaid="iBioSim18" value="0.033"/>
-      <parameter id="ko_r" constant="true" name="Reverse RNAP binding rate" metaid="iBioSim19" value="1"/>
-      <parameter id="kao_f" constant="true" name="Forward activated RNAP binding rate" metaid="iBioSim20" value="1"/>
-      <parameter id="kao_r" constant="true" name="Reverse activated RNAP binding rate" metaid="iBioSim21" value="1"/>
-      <parameter id="kmdiff_f" constant="true" name="Forward membrane diffusion rate" metaid="iBioSim22" value="1"/>
-      <parameter id="kmdiff_r" constant="true" name="Reverse membrane diffusion rate" metaid="iBioSim23" value="0.01"/>
-      <parameter id="kd" constant="true" name="Degradation rate" metaid="iBioSim24" value="0.0075"/>
-      <parameter id="kecd" constant="true" name="Extracellular degradation rate" metaid="iBioSim25" value="0.005"/>
-      <parameter id="nc" constant="true" name="Stoichiometry of binding" metaid="iBioSim26" value="2"/>
-      <parameter id="nr" constant="true" name="Initial RNAP count" metaid="iBioSim27" value="30"/>
-      <parameter id="ko" constant="true" name="Open complex production rate" metaid="iBioSim28" value="0.05"/>
-      <parameter id="kb" constant="true" name="Basal production rate" metaid="iBioSim29" value="0.0001"/>
-      <parameter id="ng" constant="true" name="Initial promoter count" metaid="iBioSim30" value="2"/>
-      <parameter id="np" constant="true" name="Stoichiometry of production" metaid="iBioSim31" value="10"/>
-      <parameter id="ka" constant="true" name="Activated production rate" metaid="iBioSim32" value="0.25"/>
-      <parameter id="kecdiff" constant="true" name="Extracellular diffusion rate" metaid="iBioSim33" value="1"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="Condition_0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <ci> F </ci>
-            <apply>
-              <leq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 2100 </cn>
-            </apply>
-            <apply>
-              <and/>
-              <apply>
-                <gt/>
-                <ci> S2 </ci>
-                <cn type="integer"> 80 </cn>
-              </apply>
-              <apply>
-                <lt/>
-                <ci> S3 </ci>
-                <cn type="integer"> 20 </cn>
-              </apply>
-            </apply>
-          </apply>
-        </math>
-        <message>
-        <p xmlns="http://www.w3.org/1999/xhtml">Pr=?{(true)PU[0,2100]((S2 greater than 80) and (S3 less than 20))}</p>        </message>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction id="Degradation_S3" metaid="iBioSim44" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="S3" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> S3 </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_S4" metaid="iBioSim45" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="S4" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> S4 </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_CC" metaid="iBioSim48" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="CC" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> CC </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_S2" metaid="iBioSim49" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="S2" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> S2 </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_S1" metaid="iBioSim50" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="S1" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> S1 </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_Y" metaid="iBioSim51" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="Y" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Y </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_XX" metaid="iBioSim52" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="XX" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> XX </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_Z" metaid="iBioSim53" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="Z" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Z </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P9" metaid="iBioSim54" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="CC" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P9" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="Z" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P9 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> Z </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P8" metaid="iBioSim55" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-          <speciesReference constant="true" species="S2" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P8" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="S3" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P8 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> S3 </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P5" metaid="iBioSim56" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S2" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P5" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="S1" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P5 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> S1 </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P4" metaid="iBioSim57" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S1" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P4" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="XX" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P4 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> XX </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P7" metaid="iBioSim58" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S1" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P7" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="Y" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P7 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> Y </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P6" metaid="iBioSim59" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S3" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P6" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="S2" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P6 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> S2 </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P1" metaid="iBioSim60" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S4" stoichiometry="10"/>
-          <speciesReference constant="true" species="XX" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P1" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="AA" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P1 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> AA </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P3" metaid="iBioSim61" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S3" stoichiometry="10"/>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P3" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="S4" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P3 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> S4 </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P2" metaid="iBioSim62" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S4" stoichiometry="10"/>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P2" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="B" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P2 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> B </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P10" metaid="iBioSim63" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="S4" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P10" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="S2" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P10 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> S2 </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <listOfEvents>
-      <event id="event0" metaid="iBioSim1" useValuesFromTriggerTime="false">
-        <trigger persistent="false" initialValue="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 5000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 0 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="AA">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 40 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="event1" metaid="iBioSim47" useValuesFromTriggerTime="false">
-        <trigger persistent="false" initialValue="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 10000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 0 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="B">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 40 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="event2" metaid="iBioSim64" useValuesFromTriggerTime="false">
-        <trigger persistent="false" initialValue="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 15000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 0 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="AA">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="event3" metaid="iBioSim65" useValuesFromTriggerTime="false">
-        <trigger persistent="false" initialValue="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 20000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 0 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="B">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props
index ef52047..f8f8ec4 100644
--- a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props
+++ b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.props
@@ -1,2 +1,4 @@
 // Probability that the toggle switch changes state erroneously within T time units.
-"change_state" : P=? [ F<=2100 ((S2 > 80) & (S3 < 20))]
+// "change_state" : P=? [ F<=2100 ((S2 > 80) & (S3 < 20))]
+
+P=? [ true U[0,50] (S3 <= 65) ]
diff --git a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml
index 7b0a500..a11cc34 100644
--- a/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml
+++ b/GeneticCircuits/Muller_C_Element/Speed_Independent_10_10/Speed_Independent_10_10.xml
@@ -1,940 +1,8 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="2" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="Speed_Independent" metaid="iBioSim11">
-    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
-      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
-      <comp:port comp:id="input__A" comp:idRef="A" sboTerm="SBO:0000600"/>
-      <comp:port comp:id="input__B" comp:idRef="B" sboTerm="SBO:0000600"/>
-      <comp:port comp:id="output__C" comp:idRef="C" sboTerm="SBO:0000601"/>
-      <comp:port comp:id="reaction__Degradation_C" comp:idRef="Degradation_C" sboTerm="SBO:0000601"/>
-    </comp:listOfPorts>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
-            <layout:boundingBox>
-              <layout:position layout:x="527" layout:y="313"/>
-              <layout:dimensions layout:height="40" layout:width="50"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__S3" layout:id="Glyph__c0__substrate__S3" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="650" layout:y="52"/>
-                      <layout:end layout:x="552" layout:y="333"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-              <layout:referenceGlyph layout:glyph="Glyph__S2" layout:id="Glyph__c0__substrate__S2" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="950" layout:y="120"/>
-                      <layout:end layout:x="552" layout:y="333"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__A" layout:species="A">
-            <layout:boundingBox>
-              <layout:position layout:x="30" layout:y="180"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__S1" layout:species="S1">
-            <layout:boundingBox>
-              <layout:position layout:x="600" layout:y="105"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__S2" layout:species="S2">
-            <layout:boundingBox>
-              <layout:position layout:x="900" layout:y="105"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__S3" layout:species="S3">
-            <layout:boundingBox>
-              <layout:position layout:x="600" layout:y="37"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__S4" layout:species="S4">
-            <layout:boundingBox>
-              <layout:position layout:x="300" layout:y="75"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
-            <layout:boundingBox>
-              <layout:position layout:x="190" layout:y="260"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Y" layout:species="Y">
-            <layout:boundingBox>
-              <layout:position layout:x="300" layout:y="135"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__Z" layout:species="Z">
-            <layout:boundingBox>
-              <layout:position layout:x="900" layout:y="15"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
-            <layout:boundingBox>
-              <layout:position layout:x="880" layout:y="360"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__P10" layout:species="P10">
-            <layout:boundingBox>
-              <layout:position layout:x="603" layout:y="62"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__P1" layout:species="P1">
-            <layout:boundingBox>
-              <layout:position layout:x="150" layout:y="45"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__P2" layout:species="P2">
-            <layout:boundingBox>
-              <layout:position layout:x="150" layout:y="105"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
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-      <functionDefinition id="F" name="Eventually Property">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
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             <bvar>
@@ -956,53 +24,53 @@
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-    <listOfConstraints>
-      <constraint metaid="c0">
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+      <addedPrefix:compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
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+    <addedPrefix:listOfSpecies>
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+      <addedPrefix:species metaid="iBioSim4" id="S2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim5" id="S3" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim6" id="S4" compartment="Cell" initialAmount="130" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim7" id="B" compartment="Cell" initialAmount="120" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
+      <addedPrefix:species metaid="iBioSim8" id="Y" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim9" id="Z" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim10" id="C" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim12" id="P10" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim14" id="P1" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim16" id="P2" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim18" id="P3" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim20" id="P4" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim22" id="P5" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim24" id="P6" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim26" id="P7" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim28" id="P8" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim30" id="P9" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim33" id="X" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim2" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim13" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim34" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim35" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim36" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim37" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim38" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim39" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim40" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim41" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim42" id="nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim43" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim44" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim45" id="ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim46" id="np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim47" id="ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <ci> F </ci>
@@ -1026,14 +94,14 @@
             </apply>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="Degradation_S4" metaid="iBioSim48" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="S4" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim48" id="Degradation_S4" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="S4" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1041,13 +109,13 @@
               <ci> S4 </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_S1" metaid="iBioSim49" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="S1" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim49" id="Degradation_S1" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="S1" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1055,13 +123,13 @@
               <ci> S1 </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_Z" metaid="iBioSim53" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim53" id="Degradation_Z" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1069,13 +137,13 @@
               <ci> Z </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_C" metaid="iBioSim54" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="C" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim54" id="Degradation_C" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="C" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1083,51 +151,42 @@
               <ci> C </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P10" metaid="iBioSim32" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S4" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P10"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="S2"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim32" sboTerm="SBO:0000589" id="Production_P10" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S4" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P10"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="S2"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P10 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P10 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1145,52 +204,43 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P1" metaid="iBioSim15" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S4" stoichiometry="10"/>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim15" sboTerm="SBO:0000589" id="Production_P1" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S4" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P1 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P1 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1208,52 +258,43 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P2" metaid="iBioSim17" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S4" stoichiometry="10"/>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim17" sboTerm="SBO:0000589" id="Production_P2" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S4" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P2 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P2 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1271,52 +312,43 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P3" metaid="iBioSim19" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S3" stoichiometry="10"/>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="S4"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim19" sboTerm="SBO:0000589" id="Production_P3" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S3" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="S4"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P3 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P3 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1334,51 +366,42 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P4" metaid="iBioSim21" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S1" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim21" sboTerm="SBO:0000589" id="Production_P4" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S1" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P4 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P4 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1396,51 +419,42 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P5" metaid="iBioSim23" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S2" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="S1"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim23" sboTerm="SBO:0000589" id="Production_P5" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S2" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="S1"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P5 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P5 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1458,51 +472,42 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P6" metaid="iBioSim25" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S3" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="S2"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim25" sboTerm="SBO:0000589" id="Production_P6" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S3" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="S2"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P6 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P6 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1520,51 +525,42 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P7" metaid="iBioSim27" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S1" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim27" sboTerm="SBO:0000589" id="Production_P7" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S1" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P7 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P7 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1582,52 +578,43 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P8" metaid="iBioSim29" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="S2" stoichiometry="10"/>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="S3"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim29" sboTerm="SBO:0000589" id="Production_P8" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="S2" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="S3"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P8 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P8 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1645,51 +632,42 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P9" metaid="iBioSim31" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="C" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P9"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim31" sboTerm="SBO:0000589" id="Production_P9" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="C" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P9"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
               <apply>
                 <times/>
+                <ci> P9 </ci>
+                <ci> ko </ci>
                 <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> P9 </ci>
-                    <ci> ko </ci>
-                  </apply>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
                 </apply>
                 <ci> nr </ci>
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1707,13 +685,13 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_X" metaid="iBioSim55" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim55" id="Degradation_X" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1721,13 +699,13 @@
               <ci> X </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_S2" metaid="iBioSim50" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="S2" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim50" id="Degradation_S2" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="S2" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1735,13 +713,13 @@
               <ci> S2 </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_S3" metaid="iBioSim51" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="S3" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim51" id="Degradation_S3" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="S3" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1749,13 +727,13 @@
               <ci> S3 </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_Y" metaid="iBioSim52" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim52" id="Degradation_Y" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1763,8 +741,8 @@
               <ci> Y </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.props b/GeneticCircuits/Muller_C_Element/Toggle/Toggle.props
deleted file mode 100644
index d845eda..0000000
--- a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.props
+++ /dev/null
@@ -1,2 +0,0 @@
-// Probability that the toggle switch changes state erroneously within T time units.
-"change_state" : P=? [ F<=2100 ((Y < 40) & (Z > 80))]
diff --git a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.sm b/GeneticCircuits/Muller_C_Element/Toggle/Toggle.sm
deleted file mode 100644
index fea4690..0000000
--- a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.sm
+++ /dev/null
@@ -1,295 +0,0 @@
-// File generated by automatic SBML-to-PRISM conversion
-// Original SBML file: toggle.xml
-
-ctmc
-
-const int MAX_AMOUNT = 200;
-
-// Compartment size
-const double default = 1.0;
-
-// Model parameters
-const double kr_f = 0.5; // kr_f
-const double kr_r = 1; // kr_r
-const double ka_f = 0.0033; // ka_f
-const double ka_r = 1; // ka_r
-const double kc_f = 0.05; // kc_f
-const double kc_r = 1; // kc_r
-const double ko_f = 0.033; // ko_f
-const double ko_r = 1; // ko_r
-const double kao_f = 1; // kao_f
-const double kao_r = 1; // kao_r
-const double kmdiff_f = 1; // kmdiff_f
-const double kmdiff_r = 0.01; // kmdiff_r
-const double kd = 0.0075; // kd
-const double kecd = 0.005; // kecd
-const double nc = 2; // nc
-const double nr = 30; // nr
-const double ko = 0.05; // ko
-const double kb = 0.0001; // kb
-const double ng = 2; // ng
-const double np = 10; // np
-const double ka = 0.25; // ka
-const double kecdiff = 1; // kecdiff
-
-// Species AA
-const int AA_MAX = MAX_AMOUNT;
-module AA
-	
-	AA : [0..AA_MAX] init 0; // Initial amount 0
-	
-	
-endmodule
-
-// Species B
-const int B_MAX = MAX_AMOUNT;
-module B
-	
-	B : [0..B_MAX] init 120; // Initial amount 120
-	
-	
-endmodule
-
-// Species Cout
-const int Cout_MAX = MAX_AMOUNT;
-module Cout
-	
-	Cout : [0..Cout_MAX] init 120; // Initial amount 120
-	
-	// Degradation_Cout
-	[Degradation_Cout] Cout > 0 -> (Cout'=Cout-1);
-	// Production_P5
-	[Production_P5]  Cout <= Cout_MAX-10 -> (Cout'=Cout+10);
-	
-endmodule
-
-// Species D
-const int D_MAX = MAX_AMOUNT;
-module D
-	
-	D : [0..D_MAX] init 0; // Initial amount 0
-	
-	// Degradation_D
-	[Degradation_D] D > 0 -> (D'=D-1);
-	// Production_P1
-	[Production_P1]  D <= D_MAX-10 -> (D'=D+10);
-	
-endmodule
-
-// Species EE
-const int EE_MAX = MAX_AMOUNT;
-module EE
-	
-	EE : [0..EE_MAX] init 0; // Initial amount 0
-	
-	// Degradation_EE
-	[Degradation_EE] EE > 0 -> (EE'=EE-1);
-	// Production_P2
-	[Production_P2]  EE <= EE_MAX-10 -> (EE'=EE+10);
-	
-endmodule
-
-// Species FF
-const int FF_MAX = MAX_AMOUNT;
-module FF
-	
-	FF : [0..FF_MAX] init 200; // Initial amount 200
-	
-	// Degradation_FF
-	[Degradation_FF] FF > 0 -> (FF'=FF-1);
-	// Production_P8
-	[Production_P8]  FF <= FF_MAX-10 -> (FF'=FF+10);
-	// Production_P7
-	[Production_P7]  FF <= FF_MAX-10 -> (FF'=FF+10);
-	
-endmodule
-
-// Species XX
-const int XX_MAX = MAX_AMOUNT;
-module XX
-	
-	XX : [0..XX_MAX] init 0; // Initial amount 0
-	
-	// Degradation_XX
-	[Degradation_XX] XX > 0 -> (XX'=XX-1);
-	// Production_P1
-	[Production_P1]  XX <= XX_MAX-10 -> (XX'=XX+10);
-	// Production_P2
-	[Production_P2]  XX <= XX_MAX-10 -> (XX'=XX+10);
-	
-endmodule
-
-// Species Y
-const int Y_MAX = MAX_AMOUNT;
-module Y
-	
-	Y : [0..Y_MAX] init 200; // Initial amount 200
-	
-	// Degradation_Y
-	[Degradation_Y] Y > 0 -> (Y'=Y-1);
-	// Production_P5
-	[Production_P5]  Y <= Y_MAX-10 -> (Y'=Y+10);
-	// Production_P3
-	[Production_P3]  Y <= Y_MAX-10 -> (Y'=Y+10);
-	
-endmodule
-
-// Species Z
-const int Z_MAX = MAX_AMOUNT;
-module Z
-	
-	Z : [0..Z_MAX] init 0; // Initial amount 0
-	
-	// Degradation_Z
-	[Degradation_Z] Z > 0 -> (Z'=Z-1);
-	// Production_P4
-	[Production_P4]  Z <= Z_MAX-10 -> (Z'=Z+10);
-	// Production_P6
-	[Production_P6]  Z <= Z_MAX-10 -> (Z'=Z+10);
-	
-endmodule
-
-// Species P8
-const int P8_MAX = MAX_AMOUNT;
-module P8
-	
-	P8 : [0..P8_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Species P5
-const int P5_MAX = MAX_AMOUNT;
-module P5
-	
-	P5 : [0..P5_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Species P4
-const int P4_MAX = MAX_AMOUNT;
-module P4
-	
-	P4 : [0..P4_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Species P7
-const int P7_MAX = MAX_AMOUNT;
-module P7
-	
-	P7 : [0..P7_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Species P6
-const int P6_MAX = MAX_AMOUNT;
-module P6
-	
-	P6 : [0..P6_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Species P1
-const int P1_MAX = MAX_AMOUNT;
-module P1
-	
-	P1 : [0..P1_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Species P3
-const int P3_MAX = MAX_AMOUNT;
-module P3
-	
-	P3 : [0..P3_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Species P2
-const int P2_MAX = MAX_AMOUNT;
-module P2
-	
-	P2 : [0..P2_MAX] init 2; // Initial amount 2
-	
-	
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-	// Degradation_D: D -> 
-	[Degradation_D] (kd*D) > 0 -> (kd*D) : true;
-	// Degradation_EE: EE -> 
-	[Degradation_EE] (kd*EE) > 0 -> (kd*EE) : true;
-	// Degradation_FF: FF -> 
-	[Degradation_FF] (kd*FF) > 0 -> (kd*FF) : true;
-	// Degradation_Cout: Cout -> 
-	[Degradation_Cout] (kd*Cout) > 0 -> (kd*Cout) : true;
-	// Degradation_Y: Y -> 
-	[Degradation_Y] (kd*Y) > 0 -> (kd*Y) : true;
-	// Degradation_XX: XX -> 
-	[Degradation_XX] (kd*XX) > 0 -> (kd*XX) : true;
-	// Degradation_Z: Z -> 
-	[Degradation_Z] (kd*Z) > 0 -> (kd*Z) : true;
-	// Production_P8:  -> FF
-	[Production_P8] (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*EE),nc)))) > 0 -> (((((P8*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*EE),nc)))) : true;
-	// Production_P5:  -> Y+Cout
-	[Production_P5] (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) > 0 -> (((((P5*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Z),nc)))) : true;
-	// Production_P4:  -> Z
-	[Production_P4] (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*FF),nc)))) > 0 -> (((((P4*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*FF),nc)))) : true;
-	// Production_P7:  -> FF
-	[Production_P7] (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*D),nc)))) > 0 -> (((((P7*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*D),nc)))) : true;
-	// Production_P6:  -> Z
-	[Production_P6] (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) > 0 -> (((((P6*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*Y),nc)))) : true;
-	// Production_P1:  -> D+XX
-	[Production_P1] (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) > 0 -> (((((P1*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*AA),nc)))) : true;
-	// Production_P3:  -> Y
-	[Production_P3] (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) > 0 -> (((((P3*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*XX),nc)))) : true;
-	// Production_P2:  -> EE+XX
-	[Production_P2] (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) > 0 -> (((((P2*ko)*ko_f)/ko_r)*nr)/((1+((ko_f/ko_r)*nr))+(func(pow,((kr_f/kr_r)*B),nc)))) : true;
-
-endmodule
-
-// Reward structures (one per species)
-
-// Reward 1: AA
-rewards "AA" true : AA; endrewards
-// Reward 2: B
-rewards "B" true : B; endrewards
-// Reward 3: Cout
-rewards "Cout" true : Cout; endrewards
-// Reward 4: D
-rewards "D" true : D; endrewards
-// Reward 5: EE
-rewards "EE" true : EE; endrewards
-// Reward 6: FF
-rewards "FF" true : FF; endrewards
-// Reward 7: XX
-rewards "XX" true : XX; endrewards
-// Reward 8: Y
-rewards "Y" true : Y; endrewards
-// Reward 9: Z
-rewards "Z" true : Z; endrewards
-// Reward 10: P8
-rewards "P8" true : P8; endrewards
-// Reward 11: P5
-rewards "P5" true : P5; endrewards
-// Reward 12: P4
-rewards "P4" true : P4; endrewards
-// Reward 13: P7
-rewards "P7" true : P7; endrewards
-// Reward 14: P6
-rewards "P6" true : P6; endrewards
-// Reward 15: P1
-rewards "P1" true : P1; endrewards
-// Reward 16: P3
-rewards "P3" true : P3; endrewards
-// Reward 17: P2
-rewards "P2" true : P2; endrewards
diff --git a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.xml b/GeneticCircuits/Muller_C_Element/Toggle/Toggle.xml
deleted file mode 100755
index 69fcc57..0000000
--- a/GeneticCircuits/Muller_C_Element/Toggle/Toggle.xml
+++ /dev/null
@@ -1,1137 +0,0 @@
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-  <model id="toggle" metaid="iBioSim60">
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-      <comp:port comp:idRef="Z" sboTerm="SBO:0000601" comp:id="internal__Z"/>
-      <comp:port comp:idRef="default" sboTerm="SBO:0000601" comp:id="compartment__default"/>
-      <comp:port comp:idRef="Cout" sboTerm="SBO:0000601" comp:id="output__Cout"/>
-      <comp:port comp:idRef="XX" sboTerm="SBO:0000601" comp:id="output__XX"/>
-      <comp:port comp:idRef="FF" sboTerm="SBO:0000601" comp:id="output__FF"/>
-      <comp:port comp:idRef="AA" sboTerm="SBO:0000600" comp:id="input__AA"/>
-      <comp:port comp:idRef="EE" sboTerm="SBO:0000601" comp:id="output__EE"/>
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-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:reference="event0" layout:id="Glyph__event0">
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-            <layout:listOfReferenceGlyphs>
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-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
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-      <species id="P5" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim34" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P4" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim35" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P7" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim36" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P6" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim37" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P1" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim38" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P3" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim39" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-      <species id="P2" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim40" boundaryCondition="false" sboTerm="SBO:0000590" compartment="default"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter id="kr_f" constant="true" name="Forward repression binding rate" metaid="iBioSim11" value="0.5"/>
-      <parameter id="kr_r" constant="true" name="Reverse repression binding rate" metaid="iBioSim12" value="1"/>
-      <parameter id="ka_f" constant="true" name="Forward activation binding rate" metaid="iBioSim13" value="0.0033"/>
-      <parameter id="ka_r" constant="true" name="Reverse activation binding rate" metaid="iBioSim14" value="1"/>
-      <parameter id="kc_f" constant="true" name="Forward complex formation rate" metaid="iBioSim15" value="0.05"/>
-      <parameter id="kc_r" constant="true" name="Reverse complex formation rate" metaid="iBioSim16" value="1"/>
-      <parameter id="ko_f" constant="true" name="Forward RNAP binding rate" metaid="iBioSim17" value="0.033"/>
-      <parameter id="ko_r" constant="true" name="Reverse RNAP binding rate" metaid="iBioSim18" value="1"/>
-      <parameter id="kao_f" constant="true" name="Forward activated RNAP binding rate" metaid="iBioSim19" value="1"/>
-      <parameter id="kao_r" constant="true" name="Reverse activated RNAP binding rate" metaid="iBioSim20" value="1"/>
-      <parameter id="kmdiff_f" constant="true" name="Forward membrane diffusion rate" metaid="iBioSim21" value="1"/>
-      <parameter id="kmdiff_r" constant="true" name="Reverse membrane diffusion rate" metaid="iBioSim22" value="0.01"/>
-      <parameter id="kd" constant="true" name="Degradation rate" metaid="iBioSim23" value="0.0075"/>
-      <parameter id="kecd" constant="true" name="Extracellular degradation rate" metaid="iBioSim24" value="0.005"/>
-      <parameter id="nc" constant="true" name="Stoichiometry of binding" metaid="iBioSim25" value="2"/>
-      <parameter id="nr" constant="true" name="Initial RNAP count" metaid="iBioSim26" value="30"/>
-      <parameter id="ko" constant="true" name="Open complex production rate" metaid="iBioSim27" value="0.05"/>
-      <parameter id="kb" constant="true" name="Basal production rate" metaid="iBioSim28" value="0.0001"/>
-      <parameter id="ng" constant="true" name="Initial promoter count" metaid="iBioSim29" value="2"/>
-      <parameter id="np" constant="true" name="Stoichiometry of production" metaid="iBioSim30" value="10"/>
-      <parameter id="ka" constant="true" name="Activated production rate" metaid="iBioSim31" value="0.25"/>
-      <parameter id="kecdiff" constant="true" name="Extracellular diffusion rate" metaid="iBioSim32" value="1"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction id="Degradation_D" metaid="iBioSim41" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="D" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> D </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_EE" metaid="iBioSim42" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="EE" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> EE </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_FF" metaid="iBioSim43" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="FF" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> FF </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_Cout" metaid="iBioSim46" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="Cout" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Cout </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_Y" metaid="iBioSim47" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="Y" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Y </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_XX" metaid="iBioSim48" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="XX" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> XX </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Degradation_Z" metaid="iBioSim49" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="default">
-        <listOfReactants>
-          <speciesReference constant="true" species="Z" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> Z </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P8" metaid="iBioSim50" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="FF" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P8" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="EE" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P8 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> EE </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P5" metaid="iBioSim51" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-          <speciesReference constant="true" species="Cout" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P5" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="Z" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P5 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> Z </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P4" metaid="iBioSim52" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P4" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="FF" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P4 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> FF </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P7" metaid="iBioSim53" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="FF" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P7" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="D" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P7 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> D </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P6" metaid="iBioSim54" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P6" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="Y" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P6 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> Y </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P1" metaid="iBioSim55" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="D" stoichiometry="10"/>
-          <speciesReference constant="true" species="XX" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P1" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="AA" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P1 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> AA </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P3" metaid="iBioSim56" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P3" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="XX" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P3 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> XX </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction id="Production_P2" metaid="iBioSim57" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="default">
-        <listOfProducts>
-          <speciesReference constant="true" species="EE" stoichiometry="10"/>
-          <speciesReference constant="true" species="XX" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P2" sboTerm="SBO:0000598"/>
-          <modifierSpeciesReference species="B" sboTerm="SBO:0000020"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P2 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> B </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <listOfEvents>
-      <event id="event0" metaid="iBioSim1" useValuesFromTriggerTime="false">
-        <trigger persistent="false" initialValue="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 5000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 0 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="AA">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 40 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="event1" metaid="iBioSim45" useValuesFromTriggerTime="false">
-        <trigger persistent="false" initialValue="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 10000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 0 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="B">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
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-            </math>
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diff --git a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props
index d845eda..b5f6aaa 100644
--- a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props
+++ b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.props
@@ -1,2 +1,4 @@
 // Probability that the toggle switch changes state erroneously within T time units.
-"change_state" : P=? [ F<=2100 ((Y < 40) & (Z > 80))]
+//"change_state" : P=? [ F<=2100 ((Y < 40) & (Z > 80))]
+
+P=? [ true U[0,50] (Y <= 50) ]
diff --git a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml
index 59265dc..9140703 100644
--- a/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml
+++ b/GeneticCircuits/Muller_C_Element/Toggle_10_10/Toggle_10_10.xml
@@ -1,790 +1,8 @@
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-        </layout:listOfReactionGlyphs>
-        <layout:listOfTextGlyphs>
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-        </layout:listOfTextGlyphs>
-      </layout:layout>
-    </layout:listOfLayouts>
-    <listOfFunctionDefinitions>
-      <functionDefinition id="F" name="Eventually Property">
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim42" id="Toggle_Switch_C">
+    <addedPrefix:listOfFunctionDefinitions>
+      <addedPrefix:functionDefinition id="F" name="Eventually Property">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <lambda>
             <bvar>
@@ -806,50 +24,50 @@
             </apply>
           </lambda>
         </math>
-            </functionDefinition>
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-    <listOfSpecies>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="FF" initialAmount="70" metaid="iBioSim8"/>
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-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P5" initialAmount="2" metaid="iBioSim21" sboTerm="SBO:0000590"/>
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-      <parameter constant="true" id="ko_f" metaid="iBioSim31" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="ko_r" metaid="iBioSim32" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kao_f" metaid="iBioSim33" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kao_r" metaid="iBioSim34" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim35" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="nr" metaid="iBioSim36" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="ko" metaid="iBioSim37" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="kb" metaid="iBioSim38" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="ng" metaid="iBioSim39" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="np" metaid="iBioSim40" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="ka" metaid="iBioSim41" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="kd" metaid="iBioSim12" name="Degradation rate" value="0.00075"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="c0">
+      </addedPrefix:functionDefinition>
+    </addedPrefix:listOfFunctionDefinitions>
+    <addedPrefix:listOfCompartments>
+      <addedPrefix:compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
+    </addedPrefix:listOfCompartments>
+    <addedPrefix:listOfSpecies>
+      <addedPrefix:species metaid="iBioSim1" id="A" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
+      <addedPrefix:species metaid="iBioSim3" id="D" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim4" id="B" compartment="Cell" initialAmount="120" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
+      <addedPrefix:species metaid="iBioSim5" id="Y" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim6" id="E" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim7" id="X" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim8" id="FF" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim9" id="Z" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim10" id="C" compartment="Cell" initialAmount="70" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim11" id="P8" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim13" id="P1" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim15" id="P2" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim17" id="P3" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim19" id="P4" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim21" id="P5" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim23" id="P6" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim25" id="P7" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim2" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim28" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim29" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim30" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim31" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim32" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim33" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim34" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim35" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim36" id="nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim37" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim38" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim39" id="ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim40" id="np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim41" id="ka" name="Activated production rate" value="0.25" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim12" id="kd" name="Degradation rate" value="0.00075" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="c0">
         <math xmlns="http://www.w3.org/1998/Math/MathML">
           <apply>
             <ci> F </ci>
@@ -873,18 +91,18 @@
             </apply>
           </apply>
         </math>
-            </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction compartment="Cell" id="Production_P8" metaid="iBioSim27" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="FF" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="E"/>
-        </listOfModifiers>
-        <kineticLaw>
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim27" sboTerm="SBO:0000589" id="Production_P8" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="FF" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P8"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="E"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -894,11 +112,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P8 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P8 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -907,18 +122,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -936,18 +148,18 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P1" metaid="iBioSim14" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="D" stoichiometry="10"/>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim14" sboTerm="SBO:0000589" id="Production_P1" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="D" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="A"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -957,11 +169,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P1 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P1 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -970,18 +179,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -999,18 +205,18 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P2" metaid="iBioSim16" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="E" stoichiometry="10"/>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim16" sboTerm="SBO:0000589" id="Production_P2" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="E" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="B"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1020,11 +226,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P2 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P2 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1033,18 +236,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1062,17 +262,17 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P3" metaid="iBioSim18" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim18" sboTerm="SBO:0000589" id="Production_P3" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P3"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="X"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1082,11 +282,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P3 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P3 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1095,18 +292,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1124,17 +318,17 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P4" metaid="iBioSim20" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="FF"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim20" sboTerm="SBO:0000589" id="Production_P4" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P4"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="FF"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1144,11 +338,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P4 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P4 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1157,18 +348,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1186,18 +374,18 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P5" metaid="iBioSim22" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="C" stoichiometry="10"/>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim22" sboTerm="SBO:0000589" id="Production_P5" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="C" stoichiometry="10"/>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P5"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="Z"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1207,11 +395,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P5 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P5 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1220,18 +405,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1249,17 +431,17 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P6" metaid="iBioSim24" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim24" sboTerm="SBO:0000589" id="Production_P6" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P6"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="Y"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1269,11 +451,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P6 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P6 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1282,18 +461,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1311,17 +487,17 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P7" metaid="iBioSim26" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="FF" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
-        </listOfModifiers>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim26" sboTerm="SBO:0000589" id="Production_P7" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="FF" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P7"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="D"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <divide/>
@@ -1331,11 +507,8 @@
                   <divide/>
                   <apply>
                     <times/>
-                    <apply>
-                      <times/>
-                      <ci> P7 </ci>
-                      <ci> ko </ci>
-                    </apply>
+                    <ci> P7 </ci>
+                    <ci> ko </ci>
                     <ci> ko_f </ci>
                   </apply>
                   <ci> ko_r </ci>
@@ -1344,18 +517,15 @@
               </apply>
               <apply>
                 <plus/>
+                <cn type="integer"> 1 </cn>
                 <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
+                  <times/>
                   <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
                   </apply>
+                  <ci> nr </ci>
                 </apply>
                 <apply>
                   <power/>
@@ -1373,13 +543,13 @@
               </apply>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_E" metaid="iBioSim43" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="E" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim43" id="Degradation_E" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="E" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1387,13 +557,13 @@
               <ci> E </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_C" metaid="iBioSim44" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="C" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim44" id="Degradation_C" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="C" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1401,13 +571,13 @@
               <ci> C </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_X" metaid="iBioSim45" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="X" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim45" id="Degradation_X" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="X" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1415,13 +585,13 @@
               <ci> X </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_D" metaid="iBioSim46" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="D" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim46" id="Degradation_D" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="D" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1429,13 +599,13 @@
               <ci> D </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_FF" metaid="iBioSim47" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="FF" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim47" id="Degradation_FF" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="FF" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1443,13 +613,13 @@
               <ci> FF </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_Y" metaid="iBioSim48" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="Y" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim48" id="Degradation_Y" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="Y" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1457,13 +627,13 @@
               <ci> Y </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_Z" metaid="iBioSim49" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="Z" stoichiometry="10"/>
-        </listOfReactants>
-        <kineticLaw>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim49" id="Degradation_Z" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="Z" stoichiometry="10"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
           <math xmlns="http://www.w3.org/1998/Math/MathML">
             <apply>
               <times/>
@@ -1471,8 +641,8 @@
               <ci> Z </ci>
             </apply>
           </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-  </model>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
 </sbml>
diff --git a/GeneticCircuits/Repressilator/Default/Repressilator.xml b/GeneticCircuits/Repressilator/Default/Repressilator.xml
deleted file mode 100755
index 3d179f9..0000000
--- a/GeneticCircuits/Repressilator/Default/Repressilator.xml
+++ /dev/null
@@ -1,466 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2" layout:required="false" comp:required="true" fbc:required="false" arrays:required="true">
-  <model metaid="iBioSim30" id="repressilator">
-    <listOfFunctionDefinitions>
-      <functionDefinition id="St" name="Steady State Property">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <apply>
-              <not/>
-              <apply>
-                <not/>
-                <ci> x </ci>
-              </apply>
-            </apply>
-          </lambda>
-        </math>
-      </functionDefinition>
-      <functionDefinition id="PF" name="Probabilistic Eventually Property">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <lambda>
-            <bvar>
-              <ci> t </ci>
-            </bvar>
-            <bvar>
-              <ci> x </ci>
-            </bvar>
-            <apply>
-              <ci> uniform </ci>
-              <cn type="integer"> 0 </cn>
-              <cn type="integer"> 1 </cn>
-            </apply>
-          </lambda>
-        </math>
-      </functionDefinition>
-    </listOfFunctionDefinitions>
-    <listOfCompartments>
-      <compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species metaid="iBioSim2" id="CI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim3" id="LacI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim4" id="TetR" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim6" sboTerm="SBO:0000590" id="P0" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim7" sboTerm="SBO:0000590" id="P1" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-      <species metaid="iBioSim8" sboTerm="SBO:0000590" id="P2" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter metaid="iBioSim5" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
-      <parameter metaid="iBioSim9" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
-      <parameter metaid="iBioSim10" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim11" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
-      <parameter metaid="iBioSim12" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim13" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
-      <parameter metaid="iBioSim14" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim15" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim16" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
-      <parameter metaid="iBioSim17" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
-      <parameter metaid="iBioSim18" id="nr" name="Initial RNAP count" value="30" constant="true"/>
-      <parameter metaid="iBioSim19" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
-      <parameter metaid="iBioSim20" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
-      <parameter metaid="iBioSim21" id="ng" name="Initial promoter count" value="2" constant="true"/>
-      <parameter metaid="iBioSim22" id="np" name="Stoichiometry of production" value="10" constant="true"/>
-      <parameter metaid="iBioSim23" id="ka" name="Activated production rate" value="0.25" constant="true"/>
-    </listOfParameters>
-    <listOfConstraints>
-      <constraint metaid="constraint0">
-        <math xmlns="http://www.w3.org/1998/Math/MathML">
-          <apply>
-            <ci> St </ci>
-            <apply>
-              <or/>
-              <apply>
-                <and/>
-                <apply>
-                  <geq/>
-                  <ci> CI </ci>
-                  <cn type="integer"> 30 </cn>
-                </apply>
-                <apply>
-                  <geq/>
-                  <apply>
-                    <ci> PF </ci>
-                    <apply>
-                      <leq/>
-                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-                      <cn type="integer"> 800 </cn>
-                    </apply>
-                    <apply>
-                      <lt/>
-                      <ci> CI </ci>
-                      <cn type="integer"> 30 </cn>
-                    </apply>
-                  </apply>
-                  <cn> 0.95 </cn>
-                </apply>
-              </apply>
-              <apply>
-                <and/>
-                <apply>
-                  <lt/>
-                  <ci> CI </ci>
-                  <cn type="integer"> 30 </cn>
-                </apply>
-                <apply>
-                  <geq/>
-                  <apply>
-                    <ci> PF </ci>
-                    <apply>
-                      <leq/>
-                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-                      <cn type="integer"> 800 </cn>
-                    </apply>
-                    <apply>
-                      <geq/>
-                      <ci> CI </ci>
-                      <cn type="integer"> 30 </cn>
-                    </apply>
-                  </apply>
-                  <cn> 0.95 </cn>
-                </apply>
-              </apply>
-            </apply>
-          </apply>
-        </math>
-      </constraint>
-    </listOfConstraints>
-    <listOfReactions>
-      <reaction metaid="iBioSim24" sboTerm="SBO:0000179" id="Degradation_CI" reversible="false" compartment="Cell">
-        <listOfReactants>
-          <speciesReference species="CI" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> CI </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim25" sboTerm="SBO:0000179" id="Degradation_LacI" reversible="false" compartment="Cell">
-        <listOfReactants>
-          <speciesReference species="LacI" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim26" sboTerm="SBO:0000179" id="Degradation_TetR" reversible="false" compartment="Cell">
-        <listOfReactants>
-          <speciesReference species="TetR" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR </ci>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim27" sboTerm="SBO:0000589" id="Production_P0" reversible="false" compartment="Cell">
-        <listOfProducts>
-          <speciesReference species="LacI" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P0"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="CI"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> P0 </ci>
-                <ci> ko </ci>
-                <apply>
-                  <divide/>
-                  <ci> ko_f </ci>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> CI </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim28" sboTerm="SBO:0000589" id="Production_P1" reversible="false" compartment="Cell">
-        <listOfProducts>
-          <speciesReference species="TetR" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="LacI"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> P1 </ci>
-                <ci> ko </ci>
-                <apply>
-                  <divide/>
-                  <ci> ko_f </ci>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> LacI </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-      <reaction metaid="iBioSim29" sboTerm="SBO:0000589" id="Production_P2" reversible="false" compartment="Cell">
-        <listOfProducts>
-          <speciesReference species="CI" stoichiometry="10" constant="true"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
-          <modifierSpeciesReference sboTerm="SBO:0000020" species="TetR"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <ci> P2 </ci>
-                <ci> ko </ci>
-                <apply>
-                  <divide/>
-                  <ci> ko_f </ci>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <cn type="integer"> 1 </cn>
-                <apply>
-                  <times/>
-                  <apply>
-                    <divide/>
-                    <ci> ko_f </ci>
-                    <ci> ko_r </ci>
-                  </apply>
-                  <ci> nr </ci>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> TetR </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:width="1070" layout:height="425"/>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:id="Glyph__Cell" layout:compartment="Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:width="1070" layout:height="425"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__CI" layout:species="CI">
-            <layout:boundingBox>
-              <layout:position layout:x="196" layout:y="106"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI" layout:species="LacI">
-            <layout:boundingBox>
-              <layout:position layout:x="464" layout:y="112"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR" layout:species="TetR">
-            <layout:boundingBox>
-              <layout:position layout:x="379" layout:y="201"/>
-              <layout:dimensions layout:width="100" layout:height="30"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__CI__repression__LacI">
-            <layout:boundingBox>
-              <layout:position layout:x="514" layout:y="127"/>
-              <layout:dimensions layout:width="0" layout:height="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__CI__repression__LacI" layout:speciesGlyph="Glyph__LacI" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
-                      <layout:start layout:x="246" layout:y="121"/>
-                      <layout:end layout:x="514" layout:y="127"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__LacI__repression__TetR">
-            <layout:boundingBox>
-              <layout:position layout:x="429" layout:y="216"/>
-              <layout:dimensions layout:width="0" layout:height="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI__repression__TetR" layout:speciesGlyph="Glyph__TetR" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
-                      <layout:start layout:x="514" layout:y="127"/>
-                      <layout:end layout:x="429" layout:y="216"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR__repression__CI">
-            <layout:boundingBox>
-              <layout:position layout:x="246" layout:y="121"/>
-              <layout:dimensions layout:width="0" layout:height="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR__repression__CI" layout:speciesGlyph="Glyph__CI" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
-                      <layout:start layout:x="429" layout:y="216"/>
-                      <layout:end layout:x="246" layout:y="121"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-        </layout:listOfReactionGlyphs>
-        <layout:listOfTextGlyphs>
-          <layout:textGlyph layout:id="TextGlyph__constraint0" layout:text="constraint0" layout:graphicalObject="Glyph__constraint0">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="218"/>
-              <layout:dimensions layout:width="50" layout:height="40"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:id="TextGlyph__" layout:graphicalObject="Glyph__">
-            <layout:boundingBox>
-              <layout:position layout:x="312" layout:y="303"/>
-              <layout:dimensions layout:width="50" layout:height="40"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-        </layout:listOfTextGlyphs>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__constraint0" layout:metaidRef="constraint0">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="218"/>
-              <layout:dimensions layout:width="50" layout:height="40"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:id="Glyph__constraint0__substrate__CI" layout:glyph="Glyph__CI" layout:role="substrate">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
-                      <layout:start layout:x="246" layout:y="121"/>
-                      <layout:end layout:x="125" layout:y="238"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-          <layout:generalGlyph layout:id="Glyph__">
-            <layout:boundingBox>
-              <layout:position layout:x="312" layout:y="303"/>
-              <layout:dimensions layout:width="50" layout:height="40"/>
-            </layout:boundingBox>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-      </layout:layout>
-    </layout:listOfLayouts>
-    <comp:listOfPorts>
-      <comp:port sboTerm="SBO:0000601" comp:idRef="Cell" comp:id="compartment__Cell"/>
-    </comp:listOfPorts>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Repressilator/Repressilator.props b/GeneticCircuits/Repressilator/Repressilator.props
new file mode 100644
index 0000000..9a5571b
--- /dev/null
+++ b/GeneticCircuits/Repressilator/Repressilator.props
@@ -0,0 +1 @@
+P=? [ true U[0,50] (CI >= 12) ]
diff --git a/GeneticCircuits/Repressilator/Default/Repressilator.sm b/GeneticCircuits/Repressilator/Repressilator.sm
similarity index 100%
rename from GeneticCircuits/Repressilator/Default/Repressilator.sm
rename to GeneticCircuits/Repressilator/Repressilator.sm
diff --git a/GeneticCircuits/Repressilator/Repressilator.xml b/GeneticCircuits/Repressilator/Repressilator.xml
new file mode 100755
index 0000000..7b71588
--- /dev/null
+++ b/GeneticCircuits/Repressilator/Repressilator.xml
@@ -0,0 +1,334 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version2" xmlns:addedPrefix="http://www.sbml.org/sbml/level3/version2/core" level="2" version="2">
+  <addedPrefix:model metaid="iBioSim30" id="repressilator">
+    <addedPrefix:listOfFunctionDefinitions>
+      <addedPrefix:functionDefinition id="St" name="Steady State Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <not/>
+              <apply>
+                <not/>
+                <ci> x </ci>
+              </apply>
+            </apply>
+          </lambda>
+        </math>
+      </addedPrefix:functionDefinition>
+      <addedPrefix:functionDefinition id="PF" name="Probabilistic Eventually Property">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <lambda>
+            <bvar>
+              <ci> t </ci>
+            </bvar>
+            <bvar>
+              <ci> x </ci>
+            </bvar>
+            <apply>
+              <ci> uniform </ci>
+              <cn type="integer"> 0 </cn>
+              <cn type="integer"> 1 </cn>
+            </apply>
+          </lambda>
+        </math>
+      </addedPrefix:functionDefinition>
+    </addedPrefix:listOfFunctionDefinitions>
+    <addedPrefix:listOfCompartments>
+      <addedPrefix:compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
+    </addedPrefix:listOfCompartments>
+    <addedPrefix:listOfSpecies>
+      <addedPrefix:species metaid="iBioSim2" id="CI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim3" id="LacI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim4" id="TetR" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim6" id="P0" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim7" id="P1" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <addedPrefix:species metaid="iBioSim8" id="P2" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+    </addedPrefix:listOfSpecies>
+    <addedPrefix:listOfParameters>
+      <addedPrefix:parameter metaid="iBioSim5" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim9" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim10" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim11" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim12" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim13" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim14" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim15" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim16" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim17" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim18" id="nr" name="Initial RNAP count" value="30" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim19" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim20" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim21" id="ng" name="Initial promoter count" value="2" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim22" id="np" name="Stoichiometry of production" value="10" constant="true"/>
+      <addedPrefix:parameter metaid="iBioSim23" id="ka" name="Activated production rate" value="0.25" constant="true"/>
+    </addedPrefix:listOfParameters>
+    <addedPrefix:listOfConstraints>
+      <addedPrefix:constraint metaid="constraint0">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <apply>
+            <ci> St </ci>
+            <apply>
+              <or/>
+              <apply>
+                <and/>
+                <apply>
+                  <geq/>
+                  <ci> CI </ci>
+                  <cn type="integer"> 30 </cn>
+                </apply>
+                <apply>
+                  <geq/>
+                  <apply>
+                    <ci> PF </ci>
+                    <apply>
+                      <leq/>
+                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+                      <cn type="integer"> 800 </cn>
+                    </apply>
+                    <apply>
+                      <lt/>
+                      <ci> CI </ci>
+                      <cn type="integer"> 30 </cn>
+                    </apply>
+                  </apply>
+                  <cn> 0.95 </cn>
+                </apply>
+              </apply>
+              <apply>
+                <and/>
+                <apply>
+                  <lt/>
+                  <ci> CI </ci>
+                  <cn type="integer"> 30 </cn>
+                </apply>
+                <apply>
+                  <geq/>
+                  <apply>
+                    <ci> PF </ci>
+                    <apply>
+                      <leq/>
+                      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+                      <cn type="integer"> 800 </cn>
+                    </apply>
+                    <apply>
+                      <geq/>
+                      <ci> CI </ci>
+                      <cn type="integer"> 30 </cn>
+                    </apply>
+                  </apply>
+                  <cn> 0.95 </cn>
+                </apply>
+              </apply>
+            </apply>
+          </apply>
+        </math>
+      </addedPrefix:constraint>
+    </addedPrefix:listOfConstraints>
+    <addedPrefix:listOfReactions>
+      <addedPrefix:reaction metaid="iBioSim24" sboTerm="SBO:0000179" id="Degradation_CI" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="CI" stoichiometry="1"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> CI </ci>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim25" sboTerm="SBO:0000179" id="Degradation_LacI" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="LacI" stoichiometry="1"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> LacI </ci>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim26" sboTerm="SBO:0000179" id="Degradation_TetR" reversible="false">
+        <addedPrefix:listOfReactants>
+          <addedPrefix:speciesReference species="TetR" stoichiometry="1"/>
+        </addedPrefix:listOfReactants>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> kd </ci>
+              <ci> TetR </ci>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim27" sboTerm="SBO:0000589" id="Production_P0" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="LacI" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P0"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="CI"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> P0 </ci>
+                <ci> ko </ci>
+                <apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <cn type="integer"> 1 </cn>
+                <apply>
+                  <times/>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                  <ci> nr </ci>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> CI </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim28" sboTerm="SBO:0000589" id="Production_P1" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="TetR" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P1"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="LacI"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> P1 </ci>
+                <ci> ko </ci>
+                <apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <cn type="integer"> 1 </cn>
+                <apply>
+                  <times/>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                  <ci> nr </ci>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> LacI </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+      <addedPrefix:reaction metaid="iBioSim29" sboTerm="SBO:0000589" id="Production_P2" reversible="false">
+        <addedPrefix:listOfProducts>
+          <addedPrefix:speciesReference species="CI" stoichiometry="10"/>
+        </addedPrefix:listOfProducts>
+        <addedPrefix:listOfModifiers>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000598" species="P2"/>
+          <addedPrefix:modifierSpeciesReference sboTerm="SBO:0000020" species="TetR"/>
+        </addedPrefix:listOfModifiers>
+        <addedPrefix:kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <divide/>
+              <apply>
+                <times/>
+                <ci> P2 </ci>
+                <ci> ko </ci>
+                <apply>
+                  <divide/>
+                  <ci> ko_f </ci>
+                  <ci> ko_r </ci>
+                </apply>
+                <ci> nr </ci>
+              </apply>
+              <apply>
+                <plus/>
+                <cn type="integer"> 1 </cn>
+                <apply>
+                  <times/>
+                  <apply>
+                    <divide/>
+                    <ci> ko_f </ci>
+                    <ci> ko_r </ci>
+                  </apply>
+                  <ci> nr </ci>
+                </apply>
+                <apply>
+                  <power/>
+                  <apply>
+                    <times/>
+                    <apply>
+                      <divide/>
+                      <ci> kr_f </ci>
+                      <ci> kr_r </ci>
+                    </apply>
+                    <ci> TetR </ci>
+                  </apply>
+                  <ci> nc </ci>
+                </apply>
+              </apply>
+            </apply>
+          </math>
+        </addedPrefix:kineticLaw>
+      </addedPrefix:reaction>
+    </addedPrefix:listOfReactions>
+  </addedPrefix:model>
+</sbml>
diff --git a/GeneticCircuits/Repressilator/results.txt b/GeneticCircuits/Repressilator/results.txt
new file mode 100644
index 0000000..86ea27e
--- /dev/null
+++ b/GeneticCircuits/Repressilator/results.txt
@@ -0,0 +1,2 @@
+0.3802594776197713
+0.38025948379759894
diff --git a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.props b/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.props
deleted file mode 100644
index 87ad135..0000000
--- a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.props
+++ /dev/null
@@ -1,4 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: Toggle_Switch.xml
-// @GeneticLogicLab
-
diff --git a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.sm b/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.sm
deleted file mode 100644
index e913ff0..0000000
--- a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.sm
+++ /dev/null
@@ -1,199 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: Toggle_Switch.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 0.0075; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double topModell_Part2_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModell_Part2_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModell_Part2_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModell_Part2_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModell_Part2_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModell_Part2_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModell_Part2_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModell_Part2_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModell_Part2_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModell_Part2_module_sub__nr = 30.0; // Initial RNAP count
-const double topModell_Part2_module_sub__ko = 0.05; // Open complex production rate
-const double topModell_Part2_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModell_Part2_module_sub__ng = 2.0; // Initial promoter count
-const double topModell_Part2_module_sub__np = 10.0; // Stoichiometry of production
-const double topModell_Part2_module_sub__ka = 0.25; // Activated production rate
-const double topModell_Part1_module_sub__kr_f = 0.5; // Forward repression binding rate
-const double topModell_Part1_module_sub__kr_r = 1.0; // Reverse repression binding rate
-const double topModell_Part1_module_sub__ka_f = 0.0033; // Forward activation binding rate
-const double topModell_Part1_module_sub__ka_r = 1.0; // Reverse activation binding rate
-const double topModell_Part1_module_sub__ko_f = 0.033; // Forward RNAP binding rate
-const double topModell_Part1_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
-const double topModell_Part1_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
-const double topModell_Part1_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
-const double topModell_Part1_module_sub__nc = 2.0; // Stoichiometry of binding
-const double topModell_Part1_module_sub__nr = 30.0; // Initial RNAP count
-const double topModell_Part1_module_sub__ko = 0.05; // Open complex production rate
-const double topModell_Part1_module_sub__kb = 1.0E-4; // Basal production rate
-const double topModell_Part1_module_sub__ng = 2.0; // Initial promoter count
-const double topModell_Part1_module_sub__np = 10.0; // Stoichiometry of production
-const double topModell_Part1_module_sub__ka = 0.25; // Activated production rate
-
-// Species IPTG
-module IPTG
-
-  IPTG  :  int init 0;
-
-		// Complex_IPTG_LacI_protein
-		[Complex_IPTG_LacI_protein] IPTG > 0 -> (IPTG' = IPTG - 2);
-
-endmodule
-
-// Species aTc
-module aTc
-
-  aTc  :  int init 0;
-
-		// Complex_aTc_TetR_protein
-		[Complex_aTc_TetR_protein] aTc > 0 -> (aTc' = aTc - 2);
-
-endmodule
-
-// Species YFP_protein
-module YFP_protein
-
-  YFP_protein  :  int init 0;
-
-		// Degradation_YFP_protein
-		[Degradation_YFP_protein] YFP_protein > 0 -> (YFP_protein' = YFP_protein - 1);
-		// R_abstracted_production_topModell_Part2_module_sub__Part2_fc
-		[R_abstracted_production_topModell_Part2_module_sub__Part2_fc] YFP_protein > 0 -> (YFP_protein' = YFP_protein + 10);
-
-endmodule
-
-// Species aTc_TetR_protein
-module aTc_TetR_protein
-
-  aTc_TetR_protein  :  int init 0;
-
-		// Degradation_aTc_TetR_protein
-		[Degradation_aTc_TetR_protein] aTc_TetR_protein > 0 -> (aTc_TetR_protein' = aTc_TetR_protein - 1);
-		// Complex_aTc_TetR_protein
-		[Complex_aTc_TetR_protein] aTc_TetR_protein > 0 -> (aTc_TetR_protein' = aTc_TetR_protein + 1);
-
-endmodule
-
-// Species LacI_protein
-module LacI_protein
-
-  LacI_protein  :  int init 0;
-
-		// Degradation_LacI_protein
-		[Degradation_LacI_protein] LacI_protein > 0 -> (LacI_protein' = LacI_protein - 1);
-		// R_abstracted_production_topModell_Part2_module_sub__Part2_fc
-		[R_abstracted_production_topModell_Part2_module_sub__Part2_fc] LacI_protein > 0 -> (LacI_protein' = LacI_protein + 10);
-		// Complex_IPTG_LacI_protein
-		[Complex_IPTG_LacI_protein] LacI_protein > 0 -> (LacI_protein' = LacI_protein - 2);
-
-endmodule
-
-// Species IPTG_LacI_protein
-module IPTG_LacI_protein
-
-  IPTG_LacI_protein  :  int init 0;
-
-		// Degradation_IPTG_LacI_protein
-		[Degradation_IPTG_LacI_protein] IPTG_LacI_protein > 0 -> (IPTG_LacI_protein' = IPTG_LacI_protein - 1);
-		// Complex_IPTG_LacI_protein
-		[Complex_IPTG_LacI_protein] IPTG_LacI_protein > 0 -> (IPTG_LacI_protein' = IPTG_LacI_protein + 1);
-
-endmodule
-
-// Species TetR_protein
-module TetR_protein
-
-  TetR_protein  :  int init 60;
-
-		// Degradation_TetR_protein
-		[Degradation_TetR_protein] TetR_protein > 0 -> (TetR_protein' = TetR_protein - 1);
-		// R_abstracted_production_topModell_Part1_module_sub__Part1_fc
-		[R_abstracted_production_topModell_Part1_module_sub__Part1_fc] TetR_protein > 0 -> (TetR_protein' = TetR_protein + 10);
-		// Complex_aTc_TetR_protein
-		[Complex_aTc_TetR_protein] TetR_protein > 0 -> (TetR_protein' = TetR_protein - 2);
-
-endmodule
-
-// Species topModell_Part2_module_sub__Part2_fc
-module topModell_Part2_module_sub__Part2_fc
-
-  topModell_Part2_module_sub__Part2_fc  :  int init 2;
-
-
-endmodule
-
-// Species topModell_Part1_module_sub__Part1_fc
-module topModell_Part1_module_sub__Part1_fc
-
-  topModell_Part1_module_sub__Part1_fc  :  int init 2;
-
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Degradation_aTc_TetR_protein:  ->  aTc_TetR_protein -> 
-		[Degradation_aTc_TetR_protein] (kd * aTc_TetR_protein) > 0 -> (kd * aTc_TetR_protein) : true;
-
-		// Degradation_YFP_protein:  ->  YFP_protein -> 
-		[Degradation_YFP_protein] (kd * YFP_protein) > 0 -> (kd * YFP_protein) : true;
-
-		// Degradation_LacI_protein:  ->  LacI_protein -> 
-		[Degradation_LacI_protein] (kd * LacI_protein) > 0 -> (kd * LacI_protein) : true;
-
-		// Degradation_IPTG_LacI_protein:  ->  IPTG_LacI_protein -> 
-		[Degradation_IPTG_LacI_protein] (kd * IPTG_LacI_protein) > 0 -> (kd * IPTG_LacI_protein) : true;
-
-		// Degradation_TetR_protein:  ->  TetR_protein -> 
-		[Degradation_TetR_protein] (kd * TetR_protein) > 0 -> (kd * TetR_protein) : true;
-
-		// R_abstracted_production_topModell_Part1_module_sub__Part1_fc:  ->   -> 
-TetR_protein
-		[R_abstracted_production_topModell_Part1_module_sub__Part1_fc] (((ko__topModell_Part1_module_sub__Part1_fc * ng__topModell_Part1_module_sub__Part1_fc) * (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) / ((1 + (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) + pow((Kr__LacI_protein_topModell_Part1_module_sub__Part1_fc * LacI_protein) , nc__LacI_protein_topModell_Part1_module_sub__Part1_fc))) > 0 -> (((ko__topModell_Part1_module_sub__Part1_fc * ng__topModell_Part1_module_sub__Part1_fc) * (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) / ((1 + (Ko__topModell_Part1_module_sub__Part1_fc * RNAP)) + pow((Kr__LacI_protein_topModell_Part1_module_sub__Part1_fc * LacI_protein) , nc__LacI_protein_topModell_Part1_module_sub__Part1_fc))) : true;
-
-		// R_abstracted_production_topModell_Part2_module_sub__Part2_fc:  ->   -> 
-YFP_protein + 
-LacI_protein
-		[R_abstracted_production_topModell_Part2_module_sub__Part2_fc] (((ko__topModell_Part2_module_sub__Part2_fc * ng__topModell_Part2_module_sub__Part2_fc) * (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) / ((1 + (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) + pow((Kr__TetR_protein_topModell_Part2_module_sub__Part2_fc * TetR_protein) , nc__TetR_protein_topModell_Part2_module_sub__Part2_fc))) > 0 -> (((ko__topModell_Part2_module_sub__Part2_fc * ng__topModell_Part2_module_sub__Part2_fc) * (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) / ((1 + (Ko__topModell_Part2_module_sub__Part2_fc * RNAP)) + pow((Kr__TetR_protein_topModell_Part2_module_sub__Part2_fc * TetR_protein) , nc__TetR_protein_topModell_Part2_module_sub__Part2_fc))) : true;
-
-		// Complex_aTc_TetR_protein:  ->  aTc + TetR_protein -> aTc_TetR_protein
-		[Complex_aTc_TetR_protein] ((((kf_c * pow(Kc , ((nc__aTc_aTc_TetR_protein + nc__TetR_protein_aTc_TetR_protein) - 2))) * pow(aTc , nc__aTc_aTc_TetR_protein)) * pow(TetR_protein , nc__TetR_protein_aTc_TetR_protein)) - (kr_c * aTc_TetR_protein)) > 0 -> ((((kf_c * pow(Kc , ((nc__aTc_aTc_TetR_protein + nc__TetR_protein_aTc_TetR_protein) - 2))) * pow(aTc , nc__aTc_aTc_TetR_protein)) * pow(TetR_protein , nc__TetR_protein_aTc_TetR_protein)) - (kr_c * aTc_TetR_protein)) : true;
-
-		// Complex_IPTG_LacI_protein:  ->  IPTG + LacI_protein -> IPTG_LacI_protein
-		[Complex_IPTG_LacI_protein] ((((kf_c * pow(Kc , ((nc__IPTG_IPTG_LacI_protein + nc__LacI_protein_IPTG_LacI_protein) - 2))) * pow(IPTG , nc__IPTG_IPTG_LacI_protein)) * pow(LacI_protein , nc__LacI_protein_IPTG_LacI_protein)) - (kr_c * IPTG_LacI_protein)) > 0 -> ((((kf_c * pow(Kc , ((nc__IPTG_IPTG_LacI_protein + nc__LacI_protein_IPTG_LacI_protein) - 2))) * pow(IPTG , nc__IPTG_IPTG_LacI_protein)) * pow(LacI_protein , nc__LacI_protein_IPTG_LacI_protein)) - (kr_c * IPTG_LacI_protein)) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: IPTG
-rewards "IPTG" true : IPTG; endrewards
-// Reward 2: aTc
-rewards "aTc" true : aTc; endrewards
-// Reward 3: YFP_protein
-rewards "YFP_protein" true : YFP_protein; endrewards
-// Reward 4: aTc_TetR_protein
-rewards "aTc_TetR_protein" true : aTc_TetR_protein; endrewards
-// Reward 5: LacI_protein
-rewards "LacI_protein" true : LacI_protein; endrewards
-// Reward 6: IPTG_LacI_protein
-rewards "IPTG_LacI_protein" true : IPTG_LacI_protein; endrewards
-// Reward 7: TetR_protein
-rewards "TetR_protein" true : TetR_protein; endrewards
-// Reward 8: topModell_Part2_module_sub__Part2_fc
-rewards "topModell_Part2_module_sub__Part2_fc" true : topModell_Part2_module_sub__Part2_fc; endrewards
-// Reward 9: topModell_Part1_module_sub__Part1_fc
-rewards "topModell_Part1_module_sub__Part1_fc" true : topModell_Part1_module_sub__Part1_fc; endrewards
diff --git a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml b/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml
deleted file mode 100644
index 4b3cc68..0000000
--- a/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml
+++ /dev/null
@@ -1,1186 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="topModell" metaid="iBioSim9" name="Created by libsbml flatten routine" substanceUnits="mole" volumeUnits="litre">
-    <annotation>
-      <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-        <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-          <rdf:Description rdf:about="#iBioSim1">
-            <mts:ModuleDefinitions>
-              <rdf:Bag>
-                <rdf:li rdf:resource="https://async.ece.utah.edu/tools/ibiosim/topModell"/>
-              </rdf:Bag>
-            </mts:ModuleDefinitions>
-          </rdf:Description>
-        </rdf:RDF>
-      </ModelToSBOL>
-    </annotation>
-      <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="310" layout:width="435"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__aTc_High" layout:reference="aTc_High">
-            <layout:boundingBox>
-              <layout:position layout:x="300" layout:y="175"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__aTc" layout:id="Glyph__aTc_High__product__aTc" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="337.5" layout:y="187.5"/>
-                      <layout:end layout:x="90" layout:y="95"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-          <layout:generalGlyph layout:id="Glyph__aTc_low" layout:reference="aTc_low">
-            <layout:boundingBox>
-              <layout:position layout:x="320" layout:y="210"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__aTc" layout:id="Glyph__aTc_low__product__aTc" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="357.5" layout:y="222.5"/>
-                      <layout:end layout:x="90" layout:y="95"/>
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-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-          <layout:generalGlyph layout:id="Glyph__IPTG_high" layout:reference="IPTG_high">
-            <layout:boundingBox>
-              <layout:position layout:x="340" layout:y="245"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__IPTG" layout:id="Glyph__IPTG_high__product__IPTG" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
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-                      <layout:start layout:x="377.5" layout:y="257.5"/>
-                      <layout:end layout:x="70" layout:y="55"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-          <layout:generalGlyph layout:id="Glyph__IPTG_low" layout:reference="IPTG_low">
-            <layout:boundingBox>
-              <layout:position layout:x="360" layout:y="280"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__IPTG" layout:id="Glyph__IPTG_low__product__IPTG" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="397.5" layout:y="292.5"/>
-                      <layout:end layout:x="70" layout:y="55"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="topModell_Part2_module_sub__Glyph__Part2_fc" layout:species="topModell_Part2_module_sub__Part2_fc">
-            <layout:boundingBox>
-              <layout:position layout:x="-1" layout:y="-1"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__IPTG" layout:species="IPTG">
-            <layout:boundingBox>
-              <layout:position layout:x="20" layout:y="40"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__aTc" layout:species="aTc">
-            <layout:boundingBox>
-              <layout:position layout:x="40" layout:y="80"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="60" layout:y="120"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
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-          <layout:speciesGlyph layout:id="Glyph__aTc_TetR_protein" layout:species="aTc_TetR_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="80" layout:y="160"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
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-          <layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
-            <layout:boundingBox>
-              <layout:position layout:x="100" layout:y="200"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
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-          <layout:speciesGlyph layout:id="Glyph__IPTG_LacI_protein" layout:species="IPTG_LacI_protein">
-            <layout:boundingBox>
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-              <layout:dimensions layout:height="30" layout:width="100"/>
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-          <layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
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-              <layout:position layout:x="140" layout:y="280"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
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-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
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-            <layout:boundingBox>
-              <layout:position layout:x="240" layout:y="60"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Degradation_TetR_protein__substrate__TetR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__TetR_protein">
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-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
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-                      <layout:end layout:x="250" layout:y="70"/>
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-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__R_abstracted_production_topModell_Part1_module_sub__Part1_fc__modifier__LacI_protein" layout:role="modifier" layout:speciesGlyph="Glyph__LacI_protein">
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-                      <layout:end layout:x="270" layout:y="100"/>
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-                <layout:curve>
-                  <layout:listOfCurveSegments>
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-                <layout:curve>
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-                      <layout:end layout:x="290" layout:y="130"/>
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-                    <rdf:li rdf:resource="https://async.ece.utah.edu/tools/ibiosim/Part2/1"/>
-                  </rdf:Bag>
-                </mts:ComponentDefinitions>
-                <mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="https://async.ece.utah.edu/tools/ibiosim/Part2/1"/>
-                  </rdf:Bag>
-                </mts:FunctionalComponents>
-                <mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="https://async.ece.utah.edu/tools/ibiosim/Part2/1"/>
-                  </rdf:Seq>
-                </mts:DNAComponents>
-                <mts:Strand>+</mts:Strand>
-              </rdf:Description>
-            </rdf:RDF>
-          </ModelToSBOL>
-        </annotation>
-            </species>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModell_Part1_module_sub__Part1_fc" initialAmount="2" metaid="topModell_Part1_module_sub__iBioSim2" sboTerm="SBO:0000590">
-        <annotation>
-          <ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
-            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
-              <rdf:Description rdf:about="#iBioSim2">
-                <mts:ComponentDefinitions>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="https://async.ece.utah.edu/tools/ibiosim/Part1/1"/>
-                  </rdf:Bag>
-                </mts:ComponentDefinitions>
-                <mts:FunctionalComponents>
-                  <rdf:Bag>
-                    <rdf:li rdf:resource="https://async.ece.utah.edu/tools/ibiosim/Part1/1"/>
-                  </rdf:Bag>
-                </mts:FunctionalComponents>
-                <mts:DNAComponents>
-                  <rdf:Seq>
-                    <rdf:li rdf:resource="https://async.ece.utah.edu/tools/ibiosim/Part1/1"/>
-                  </rdf:Seq>
-                </mts:DNAComponents>
-                <mts:Strand>+</mts:Strand>
-              </rdf:Description>
-            </rdf:RDF>
-          </ModelToSBOL>
-        </annotation>
-            </species>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.0075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim30" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim31" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim32" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__kr_f" metaid="iBioSim24" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__kr_r" metaid="iBioSim25" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__ka_f" metaid="iBioSim27" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__ka_r" metaid="iBioSim28" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__ko_f" metaid="iBioSim29" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__ko_r" metaid="iBioSim38" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__kao_f" metaid="iBioSim39" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__kao_r" metaid="iBioSim42" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__nc" metaid="iBioSim43" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__nr" metaid="iBioSim44" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__ko" metaid="iBioSim45" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__kb" metaid="iBioSim46" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__ng" metaid="iBioSim47" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__np" metaid="iBioSim48" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModell_Part2_module_sub__ka" metaid="iBioSim49" name="Activated production rate" value="0.25"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__kr_f" metaid="iBioSim50" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__kr_r" metaid="iBioSim51" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__ka_f" metaid="iBioSim52" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__ka_r" metaid="iBioSim53" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__ko_f" metaid="iBioSim54" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__ko_r" metaid="iBioSim55" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__kao_f" metaid="iBioSim56" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__kao_r" metaid="iBioSim57" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__nc" metaid="iBioSim58" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__nr" metaid="iBioSim59" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__ko" metaid="iBioSim60" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__kb" metaid="iBioSim61" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__ng" metaid="iBioSim62" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__np" metaid="iBioSim63" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="topModell_Part1_module_sub__ka" metaid="iBioSim64" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction compartment="Cell" id="Degradation_aTc_TetR_protein" metaid="iBioSim10" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="aTc_TetR_protein" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> aTc_TetR_protein </ci>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="kd" units="u_1_second_n1" value="0.0075"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_YFP_protein" metaid="iBioSim11" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="YFP_protein" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> YFP_protein </ci>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="kd" units="u_1_second_n1" value="0.0075"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_LacI_protein" metaid="iBioSim12" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="LacI_protein" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI_protein </ci>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="kd" units="u_1_second_n1" value="0.0075"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_IPTG_LacI_protein" metaid="iBioSim13" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="IPTG_LacI_protein" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> IPTG_LacI_protein </ci>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="kd" units="u_1_second_n1" value="0.0075"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_TetR_protein" metaid="iBioSim14" reversible="false">
-        <listOfReactants>
-          <speciesReference constant="true" species="TetR_protein" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR_protein </ci>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="kd" units="u_1_second_n1" value="0.0075"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="R_abstracted_production_topModell_Part1_module_sub__Part1_fc" metaid="iBioSim15" reversible="false">
-        <listOfProducts>
-          <speciesReference constant="true" species="TetR_protein" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="LacI_protein"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <times/>
-                  <ci> ko__topModell_Part1_module_sub__Part1_fc </ci>
-                  <ci> ng__topModell_Part1_module_sub__Part1_fc </ci>
-                </apply>
-                <apply>
-                  <times/>
-                  <ci> Ko__topModell_Part1_module_sub__Part1_fc </ci>
-                  <ci> RNAP </ci>
-                </apply>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <ci> Ko__topModell_Part1_module_sub__Part1_fc </ci>
-                    <ci> RNAP </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <ci> Kr__LacI_protein_topModell_Part1_module_sub__Part1_fc </ci>
-                    <ci> LacI_protein </ci>
-                  </apply>
-                  <ci> nc__LacI_protein_topModell_Part1_module_sub__Part1_fc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="RNAP" units="u_1_mole_n1" value="30"/>
-            <localParameter id="ng__topModell_Part1_module_sub__Part1_fc" units="u_1_mole_n1" value="2"/>
-            <localParameter id="Ko__topModell_Part1_module_sub__Part1_fc" units="u_1_mole_n1" value="0.033"/>
-            <localParameter id="ko__topModell_Part1_module_sub__Part1_fc" units="u_1_second_n1" value="0.05"/>
-            <localParameter id="nc__LacI_protein_topModell_Part1_module_sub__Part1_fc" units="dimensionless" value="2"/>
-            <localParameter id="Kr__LacI_protein_topModell_Part1_module_sub__Part1_fc" units="u_1_mole_n1" value="0.5"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="R_abstracted_production_topModell_Part2_module_sub__Part2_fc" metaid="iBioSim16" reversible="false">
-        <listOfProducts>
-          <speciesReference constant="true" species="YFP_protein" stoichiometry="10"/>
-          <speciesReference constant="true" species="LacI_protein" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="TetR_protein"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <times/>
-                  <ci> ko__topModell_Part2_module_sub__Part2_fc </ci>
-                  <ci> ng__topModell_Part2_module_sub__Part2_fc </ci>
-                </apply>
-                <apply>
-                  <times/>
-                  <ci> Ko__topModell_Part2_module_sub__Part2_fc </ci>
-                  <ci> RNAP </ci>
-                </apply>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <ci> Ko__topModell_Part2_module_sub__Part2_fc </ci>
-                    <ci> RNAP </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <ci> Kr__TetR_protein_topModell_Part2_module_sub__Part2_fc </ci>
-                    <ci> TetR_protein </ci>
-                  </apply>
-                  <ci> nc__TetR_protein_topModell_Part2_module_sub__Part2_fc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="RNAP" units="u_1_mole_n1" value="30"/>
-            <localParameter id="ng__topModell_Part2_module_sub__Part2_fc" units="u_1_mole_n1" value="2"/>
-            <localParameter id="Ko__topModell_Part2_module_sub__Part2_fc" units="u_1_mole_n1" value="0.033"/>
-            <localParameter id="ko__topModell_Part2_module_sub__Part2_fc" units="u_1_second_n1" value="0.05"/>
-            <localParameter id="nc__TetR_protein_topModell_Part2_module_sub__Part2_fc" units="dimensionless" value="2"/>
-            <localParameter id="Kr__TetR_protein_topModell_Part2_module_sub__Part2_fc" units="u_1_mole_n1" value="0.5"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Complex_aTc_TetR_protein" metaid="iBioSim17" reversible="true">
-        <listOfReactants>
-          <speciesReference constant="true" species="aTc" stoichiometry="2"/>
-          <speciesReference constant="true" species="TetR_protein" stoichiometry="2"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference constant="true" species="aTc_TetR_protein" stoichiometry="1"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <minus/>
-              <apply>
-                <times/>
-                <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> kf_c </ci>
-                    <apply>
-                      <power/>
-                      <ci> Kc </ci>
-                      <apply>
-                        <minus/>
-                        <apply>
-                          <plus/>
-                          <ci> nc__aTc_aTc_TetR_protein </ci>
-                          <ci> nc__TetR_protein_aTc_TetR_protein </ci>
-                        </apply>
-                        <cn type="integer"> 2 </cn>
-                      </apply>
-                    </apply>
-                  </apply>
-                  <apply>
-                    <power/>
-                    <ci> aTc </ci>
-                    <ci> nc__aTc_aTc_TetR_protein </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <ci> TetR_protein </ci>
-                  <ci> nc__TetR_protein_aTc_TetR_protein </ci>
-                </apply>
-              </apply>
-              <apply>
-                <times/>
-                <ci> kr_c </ci>
-                <ci> aTc_TetR_protein </ci>
-              </apply>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="nc__aTc_aTc_TetR_protein" units="dimensionless" value="2"/>
-            <localParameter id="nc__TetR_protein_aTc_TetR_protein" units="dimensionless" value="2"/>
-            <localParameter id="kf_c" units="u_1_mole_n1_1_second_n1" value="0.05"/>
-            <localParameter id="Kc" units="u_1_mole_n1" value="0.05"/>
-            <localParameter id="kr_c" units="u_1_second_n1" value="1"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Complex_IPTG_LacI_protein" metaid="iBioSim18" reversible="true">
-        <listOfReactants>
-          <speciesReference constant="true" species="IPTG" stoichiometry="2"/>
-          <speciesReference constant="true" species="LacI_protein" stoichiometry="2"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference constant="true" species="IPTG_LacI_protein" stoichiometry="1"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <minus/>
-              <apply>
-                <times/>
-                <apply>
-                  <times/>
-                  <apply>
-                    <times/>
-                    <ci> kf_c </ci>
-                    <apply>
-                      <power/>
-                      <ci> Kc </ci>
-                      <apply>
-                        <minus/>
-                        <apply>
-                          <plus/>
-                          <ci> nc__IPTG_IPTG_LacI_protein </ci>
-                          <ci> nc__LacI_protein_IPTG_LacI_protein </ci>
-                        </apply>
-                        <cn type="integer"> 2 </cn>
-                      </apply>
-                    </apply>
-                  </apply>
-                  <apply>
-                    <power/>
-                    <ci> IPTG </ci>
-                    <ci> nc__IPTG_IPTG_LacI_protein </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <ci> LacI_protein </ci>
-                  <ci> nc__LacI_protein_IPTG_LacI_protein </ci>
-                </apply>
-              </apply>
-              <apply>
-                <times/>
-                <ci> kr_c </ci>
-                <ci> IPTG_LacI_protein </ci>
-              </apply>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="nc__IPTG_IPTG_LacI_protein" units="dimensionless" value="2"/>
-            <localParameter id="nc__LacI_protein_IPTG_LacI_protein" units="dimensionless" value="2"/>
-            <localParameter id="kf_c" units="u_1_mole_n1_1_second_n1" value="0.05"/>
-            <localParameter id="Kc" units="u_1_mole_n1" value="0.05"/>
-            <localParameter id="kr_c" units="u_1_second_n1" value="1"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <listOfEvents>
-      <event id="aTc_High" metaid="iBioSim22" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <true/>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 2000 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="aTc">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 60 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="aTc_low" metaid="iBioSim26" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <true/>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 4000 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="aTc">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="IPTG_high" metaid="iBioSim40" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <true/>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 6000 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="IPTG">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 60 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="IPTG_low" metaid="iBioSim41" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <true/>
-          </math>
-                </trigger>
-        <delay>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <cn type="integer"> 8000 </cn>
-          </math>
-                </delay>
-        <listOfEventAssignments>
-          <eventAssignment variable="IPTG">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Toggle_Switch/Default/jsbml.log b/GeneticCircuits/Toggle_Switch/Default/jsbml.log
deleted file mode 100644
index d568ccc..0000000
--- a/GeneticCircuits/Toggle_Switch/Default/jsbml.log
+++ /dev/null
@@ -1,130 +0,0 @@
-2023-02-02 12:06:16,124 ERROR o.s.j.x.p.SBMLCoreParser [main] Property substanceUnits is not defined in model for Level 2 and Version 2.
-2023-02-02 12:06:16,125 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = substanceUnits, value 'mole' , element name = model
-2023-02-02 12:06:16,126 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'substanceUnits' on the element model. Please check the specification for SBML.
-2023-02-02 12:06:16,127 ERROR o.s.j.x.p.SBMLCoreParser [main] Property volumeUnits is not defined in model for Level 2 and Version 2.
-2023-02-02 12:06:16,128 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = volumeUnits, value 'litre' , element name = model
-2023-02-02 12:06:16,128 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'volumeUnits' on the element model. Please check the specification for SBML.
-2023-02-02 12:06:16,129 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,171 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,172 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,173 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,175 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,176 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,177 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,178 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,221 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,222 WARN o.s.j.x.p.XMLNodeReader [main] The type of String '' on the element 'annotation' is unknown! Some data might be lost
-2023-02-02 12:06:16,228 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,229 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,229 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,230 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,230 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,231 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,235 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,236 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,236 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,236 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,237 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,237 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,237 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,238 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,239 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,239 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,240 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,240 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,241 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,241 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,241 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,242 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,242 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,242 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,243 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,243 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,243 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,244 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,244 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,244 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,244 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,245 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,245 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,245 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,246 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,246 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,246 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,246 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,247 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,247 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,247 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,249 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,250 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,250 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,250 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,251 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,251 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,251 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,252 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,252 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,252 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,254 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,255 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,255 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,255 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,255 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,256 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,256 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,256 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,256 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,256 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,257 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,257 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,257 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,258 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,259 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 2.
-2023-02-02 12:06:16,259 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:06:16,259 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:06:16,259 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,259 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,260 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,260 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,260 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,260 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,261 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 2.
-2023-02-02 12:06:16,261 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:06:16,261 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:06:16,262 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:06:16,263 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2.
-2023-02-02 12:06:16,263 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:06:16,263 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:06:16,264 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,264 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:06:16,264 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:06:16,265 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,265 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:06:16,265 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:06:16,266 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2.
-2023-02-02 12:06:16,266 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:06:16,266 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:06:16,267 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,267 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:06:16,267 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:06:16,267 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,267 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:06:16,267 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:06:16,268 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2.
-2023-02-02 12:06:16,268 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:06:16,268 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:06:16,269 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,269 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:06:16,269 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:06:16,269 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,269 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:06:16,269 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:06:16,270 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 2.
-2023-02-02 12:06:16,270 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:06:16,270 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:06:16,271 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,271 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:06:16,271 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:06:16,271 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 2.
-2023-02-02 12:06:16,271 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:06:16,271 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
diff --git a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.props b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.props
deleted file mode 100644
index dab0e7a..0000000
--- a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.props
+++ /dev/null
@@ -1,4 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: Toggle_Switch_RBA.xml
-// @GeneticLogicLab
-
diff --git a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm
deleted file mode 100644
index 2119e38..0000000
--- a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm
+++ /dev/null
@@ -1,183 +0,0 @@
-// File generated by SBML-to-PRISM converter
-// Original file: Toggle_Switch_RBA.xml
-// @GeneticLogicLab
-
-ctmc
-
-// Compartment size
-const double Cell = 1.0;
-
-// Model parameters
-const double kd = 0.0075; // Degradation rate
-const double kc_f = 0.05; // Forward complex formation rate
-const double kc_r = 1.0; // Reverse complex formation rate
-const double nc = 2.0; // Stoichiometry of binding
-const double kr_f = 0.5; // Forward repression binding rate
-const double kr_r = 1.0; // Reverse repression binding rate
-const double ka_f = 0.0033; // Forward activation binding rate
-const double ka_r = 1.0; // Reverse activation binding rate
-const double ko_f = 0.033; // Forward RNAP binding rate
-const double ko_r = 1.0; // Reverse RNAP binding rate
-const double kao_f = 1.0; // Forward activated RNAP binding rate
-const double kao_r = 1.0; // Reverse activated RNAP binding rate
-const double nr = 30.0; // Initial RNAP count
-const double ko = 0.05; // Open complex production rate
-const double kb = 1.0E-4; // Basal production rate
-const double ng = 2.0; // Initial promoter count
-const double np = 10.0; // Stoichiometry of production
-const double ka = 0.25; // Activated production rate
-
-// Species P1
-module P1
-
-  P1  :  int init 2;
-
-
-endmodule
-
-// Species IPTG
-module IPTG
-
-  IPTG  :  int init 0;
-
-		// Complex_C1
-		[Complex_C1] IPTG > 0 -> (IPTG' = IPTG - 1);
-
-endmodule
-
-// Species aTc
-module aTc
-
-  aTc  :  int init 0;
-
-		// Complex_C2
-		[Complex_C2] aTc > 0 -> (aTc' = aTc - 1);
-
-endmodule
-
-// Species TetR
-module TetR
-
-  TetR  :  int init 0;
-
-		// Degradation_TetR
-		[Degradation_TetR] TetR > 0 -> (TetR' = TetR - 1);
-		// Complex_C2
-		[Complex_C2] TetR > 0 -> (TetR' = TetR - 1);
-		// Production_P1
-		[Production_P1] TetR > 0 -> (TetR' = TetR + 10);
-
-endmodule
-
-// Species GFP
-module GFP
-
-  GFP  :  int init 0;
-
-		// Degradation_GFP
-		[Degradation_GFP] GFP > 0 -> (GFP' = GFP - 1);
-		// Production_P1
-		[Production_P1] GFP > 0 -> (GFP' = GFP + 10);
-
-endmodule
-
-// Species P2
-module P2
-
-  P2  :  int init 2;
-
-
-endmodule
-
-// Species C1
-module C1
-
-  C1  :  int init 0;
-
-		// Degradation_C1
-		[Degradation_C1] C1 > 0 -> (C1' = C1 - 1);
-		// Complex_C1
-		[Complex_C1] C1 > 0 -> (C1' = C1 + 1);
-
-endmodule
-
-// Species C2
-module C2
-
-  C2  :  int init 0;
-
-		// Degradation_C2
-		[Degradation_C2] C2 > 0 -> (C2' = C2 - 1);
-		// Complex_C2
-		[Complex_C2] C2 > 0 -> (C2' = C2 + 1);
-
-endmodule
-
-// Species LacI
-module LacI
-
-  LacI  :  int init 0;
-
-		// Degradation_LacI
-		[Degradation_LacI] LacI > 0 -> (LacI' = LacI - 1);
-		// Complex_C1
-		[Complex_C1] LacI > 0 -> (LacI' = LacI - 1);
-		// Production_P2
-		[Production_P2] LacI > 0 -> (LacI' = LacI + 10);
-
-endmodule
-
-// Reaction rates
-module reaction_rates
-
-		// Degradation_TetR:  ->  TetR -> 
-		[Degradation_TetR] (kd * TetR) > 0 -> (kd * TetR) : true;
-
-		// Degradation_GFP:  ->  GFP -> 
-		[Degradation_GFP] (kd * GFP) > 0 -> (kd * GFP) : true;
-
-		// Degradation_C2:  ->  C2 -> 
-		[Degradation_C2] (kd * C2) > 0 -> (kd * C2) : true;
-
-		// Degradation_LacI:  ->  LacI -> 
-		[Degradation_LacI] (kd * LacI) > 0 -> (kd * LacI) : true;
-
-		// Degradation_C1:  ->  C1 -> 
-		[Degradation_C1] (kd * C1) > 0 -> (kd * C1) : true;
-
-		// Complex_C1:  ->  IPTG + LacI -> C1
-		[Complex_C1] (((kc_f * pow(IPTG , nc_IPTG)) * pow(LacI , nc_LacI)) - (kc_r * C1)) > 0 -> (((kc_f * pow(IPTG , nc_IPTG)) * pow(LacI , nc_LacI)) - (kc_r * C1)) : true;
-
-		// Complex_C2:  ->  aTc + TetR -> C2
-		[Complex_C2] (((kc_f * pow(aTc , nc_aTc)) * pow(TetR , nc_TetR)) - (kc_r * C2)) > 0 -> (((kc_f * pow(aTc , nc_aTc)) * pow(TetR , nc_TetR)) - (kc_r * C2)) : true;
-
-		// Production_P1:  ->   -> 
-GFP + 
-TetR
-		[Production_P1] (((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * LacI) , nc))) > 0 -> (((((P1 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * LacI) , nc))) : true;
-
-		// Production_P2:  ->   -> 
-LacI
-		[Production_P2] (((((P2 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * TetR) , nc))) > 0 -> (((((P2 * ko) * ko_f) / ko_r) * nr) / ((1 + ((ko_f / ko_r) * nr)) + pow(((kr_f / kr_r) * TetR) , nc))) : true;
-
-endmodule
-
-// Reward structures (one per species)
-// Reward 1: P1
-rewards "P1" true : P1; endrewards
-// Reward 2: IPTG
-rewards "IPTG" true : IPTG; endrewards
-// Reward 3: aTc
-rewards "aTc" true : aTc; endrewards
-// Reward 4: TetR
-rewards "TetR" true : TetR; endrewards
-// Reward 5: GFP
-rewards "GFP" true : GFP; endrewards
-// Reward 6: P2
-rewards "P2" true : P2; endrewards
-// Reward 7: C1
-rewards "C1" true : C1; endrewards
-// Reward 8: C2
-rewards "C2" true : C2; endrewards
-// Reward 9: LacI
-rewards "LacI" true : LacI; endrewards
diff --git a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml
deleted file mode 100644
index 73a0998..0000000
--- a/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml
+++ /dev/null
@@ -1,798 +0,0 @@
-<?xml version='1.0' encoding='UTF-8' standalone='no'?>
-<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="2" version="1" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
-  <model id="ToggleSwitchCaseStudy" metaid="iBioSim15">
-    <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
-      <comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
-    </comp:listOfPorts>
-    <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-      <layout:layout layout:id="iBioSim">
-        <layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
-        <layout:listOfAdditionalGraphicalObjects>
-          <layout:generalGlyph layout:id="Glyph__IPTG_high" layout:reference="IPTG_high">
-            <layout:boundingBox>
-              <layout:position layout:x="129.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__IPTG" layout:id="Glyph__IPTG_high__product__IPTG" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="167" layout:y="15"/>
-                      <layout:end layout:x="252" layout:y="95"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-          <layout:generalGlyph layout:id="Glyph__IPTG_low" layout:reference="IPTG_low">
-            <layout:boundingBox>
-              <layout:position layout:x="234.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__IPTG" layout:id="Glyph__IPTG_low__product__IPTG" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="272" layout:y="15"/>
-                      <layout:end layout:x="252" layout:y="95"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-          <layout:generalGlyph layout:id="Glyph__aTc_high" layout:reference="aTc_high">
-            <layout:boundingBox>
-              <layout:position layout:x="339.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__aTc" layout:id="Glyph__aTc_high__product__aTc" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="377" layout:y="15"/>
-                      <layout:end layout:x="447" layout:y="95"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-          <layout:generalGlyph layout:id="Glyph__aTc_low" layout:reference="aTc_low">
-            <layout:boundingBox>
-              <layout:position layout:x="444.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-            <layout:listOfReferenceGlyphs>
-              <layout:referenceGlyph layout:glyph="Glyph__aTc" layout:id="Glyph__aTc_low__product__aTc" layout:role="product">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="482" layout:y="15"/>
-                      <layout:end layout:x="447" layout:y="95"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:referenceGlyph>
-            </layout:listOfReferenceGlyphs>
-          </layout:generalGlyph>
-        </layout:listOfAdditionalGraphicalObjects>
-        <layout:listOfCompartmentGlyphs>
-          <layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:compartmentGlyph>
-        </layout:listOfCompartmentGlyphs>
-        <layout:listOfSpeciesGlyphs>
-          <layout:speciesGlyph layout:id="Glyph__P1" layout:species="P1">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__IPTG" layout:species="IPTG">
-            <layout:boundingBox>
-              <layout:position layout:x="202" layout:y="80"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__aTc" layout:species="aTc">
-            <layout:boundingBox>
-              <layout:position layout:x="397" layout:y="80"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__TetR" layout:species="TetR">
-            <layout:boundingBox>
-              <layout:position layout:x="165" layout:y="160"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__GFP" layout:species="GFP">
-            <layout:boundingBox>
-              <layout:position layout:x="35" layout:y="160"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__P2" layout:species="P2">
-            <layout:boundingBox>
-              <layout:position layout:x="295" layout:y="160"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__C1" layout:species="C1">
-            <layout:boundingBox>
-              <layout:position layout:x="65" layout:y="155"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__C2" layout:species="C2">
-            <layout:boundingBox>
-              <layout:position layout:x="327" layout:y="240"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-          <layout:speciesGlyph layout:id="Glyph__LacI" layout:species="LacI">
-            <layout:boundingBox>
-              <layout:position layout:x="255" layout:y="320"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:speciesGlyph>
-        </layout:listOfSpeciesGlyphs>
-        <layout:listOfReactionGlyphs>
-          <layout:reactionGlyph layout:id="Glyph__Production_P1" layout:reaction="Production_P1">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="85"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Production_P1__modifier__LacI" layout:role="modifier" layout:speciesGlyph="Glyph__LacI">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="305" layout:y="335"/>
-                      <layout:end layout:x="130" layout:y="95"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Production_P1__modifier__P1" layout:role="modifier" layout:speciesGlyph="Glyph__P1">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="50" layout:y="15"/>
-                      <layout:end layout:x="130" layout:y="95"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Production_P1__product__GFP" layout:role="product" layout:speciesGlyph="Glyph__GFP">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="130" layout:y="95"/>
-                      <layout:end layout:x="85" layout:y="175"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Production_P1__product__TetR" layout:role="product" layout:speciesGlyph="Glyph__TetR">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="130" layout:y="95"/>
-                      <layout:end layout:x="215" layout:y="175"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__Production_P2" layout:reaction="Production_P2">
-            <layout:boundingBox>
-              <layout:position layout:x="215" layout:y="245"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Production_P2__modifier__P2" layout:role="modifier" layout:speciesGlyph="Glyph__P2">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="345" layout:y="175"/>
-                      <layout:end layout:x="225" layout:y="255"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Production_P2__modifier__TetR" layout:role="modifier" layout:speciesGlyph="Glyph__TetR">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="215" layout:y="175"/>
-                      <layout:end layout:x="225" layout:y="255"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-              <layout:speciesReferenceGlyph layout:id="Glyph__Production_P2__product__LacI" layout:role="product" layout:speciesGlyph="Glyph__LacI">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="225" layout:y="255"/>
-                      <layout:end layout:x="305" layout:y="335"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__IPTG__complex__C1">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="170"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__IPTG__complex__C1" layout:role="product" layout:speciesGlyph="Glyph__C1">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="252" layout:y="95"/>
-                      <layout:end layout:x="115" layout:y="170"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__LacI__complex__C1">
-            <layout:boundingBox>
-              <layout:position layout:x="115" layout:y="170"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI__complex__C1" layout:role="product" layout:speciesGlyph="Glyph__C1">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="305" layout:y="335"/>
-                      <layout:end layout:x="115" layout:y="170"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__aTc__complex__C2">
-            <layout:boundingBox>
-              <layout:position layout:x="377" layout:y="255"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__aTc__complex__C2" layout:role="product" layout:speciesGlyph="Glyph__C2">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="447" layout:y="95"/>
-                      <layout:end layout:x="377" layout:y="255"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-          <layout:reactionGlyph layout:id="Glyph__TetR__complex__C2">
-            <layout:boundingBox>
-              <layout:position layout:x="377" layout:y="255"/>
-              <layout:dimensions layout:height="0" layout:width="0"/>
-            </layout:boundingBox>
-            <layout:listOfSpeciesReferenceGlyphs>
-              <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR__complex__C2" layout:role="product" layout:speciesGlyph="Glyph__C2">
-                <layout:curve>
-                  <layout:listOfCurveSegments>
-                    <layout:curveSegment xsi:type="LineSegment">
-                      <layout:start layout:x="215" layout:y="175"/>
-                      <layout:end layout:x="377" layout:y="255"/>
-                    </layout:curveSegment>
-                  </layout:listOfCurveSegments>
-                </layout:curve>
-              </layout:speciesReferenceGlyph>
-            </layout:listOfSpeciesReferenceGlyphs>
-          </layout:reactionGlyph>
-        </layout:listOfReactionGlyphs>
-        <layout:listOfTextGlyphs>
-          <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="425" layout:width="1070"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__P1" layout:id="TextGlyph__P1" layout:text="P1">
-            <layout:boundingBox>
-              <layout:position layout:x="0" layout:y="0"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__IPTG" layout:id="TextGlyph__IPTG" layout:text="IPTG">
-            <layout:boundingBox>
-              <layout:position layout:x="202" layout:y="80"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__aTc" layout:id="TextGlyph__aTc" layout:text="aTc">
-            <layout:boundingBox>
-              <layout:position layout:x="397" layout:y="80"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__TetR" layout:id="TextGlyph__TetR" layout:text="TetR">
-            <layout:boundingBox>
-              <layout:position layout:x="165" layout:y="160"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__GFP" layout:id="TextGlyph__GFP" layout:text="GFP">
-            <layout:boundingBox>
-              <layout:position layout:x="35" layout:y="160"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__P2" layout:id="TextGlyph__P2" layout:text="P2">
-            <layout:boundingBox>
-              <layout:position layout:x="295" layout:y="160"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__C1" layout:id="TextGlyph__C1" layout:text="C1">
-            <layout:boundingBox>
-              <layout:position layout:x="65" layout:y="155"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__C2" layout:id="TextGlyph__C2" layout:text="C2">
-            <layout:boundingBox>
-              <layout:position layout:x="327" layout:y="240"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__LacI" layout:id="TextGlyph__LacI" layout:text="LacI">
-            <layout:boundingBox>
-              <layout:position layout:x="255" layout:y="320"/>
-              <layout:dimensions layout:height="30" layout:width="100"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__IPTG_high" layout:id="TextGlyph__IPTG_high" layout:text="IPTG_high">
-            <layout:boundingBox>
-              <layout:position layout:x="129.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__IPTG_low" layout:id="TextGlyph__IPTG_low" layout:text="IPTG_low">
-            <layout:boundingBox>
-              <layout:position layout:x="234.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__aTc_high" layout:id="TextGlyph__aTc_high" layout:text="aTc_high">
-            <layout:boundingBox>
-              <layout:position layout:x="339.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__aTc_low" layout:id="TextGlyph__aTc_low" layout:text="aTc_low">
-            <layout:boundingBox>
-              <layout:position layout:x="444.5" layout:y="2.5"/>
-              <layout:dimensions layout:height="25" layout:width="75"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__Production_P1" layout:id="TextGlyph__Production_P1" layout:text="Production_P1">
-            <layout:boundingBox>
-              <layout:position layout:x="120" layout:y="85"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-          <layout:textGlyph layout:graphicalObject="Glyph__Production_P2" layout:id="TextGlyph__Production_P2" layout:text="Production_P2">
-            <layout:boundingBox>
-              <layout:position layout:x="215" layout:y="245"/>
-              <layout:dimensions layout:height="20" layout:width="20"/>
-            </layout:boundingBox>
-          </layout:textGlyph>
-        </layout:listOfTextGlyphs>
-      </layout:layout>
-    </layout:listOfLayouts>
-    <listOfCompartments>
-      <compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
-    </listOfCompartments>
-    <listOfSpecies>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P1" initialAmount="2" metaid="iBioSim2"/>
-      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="IPTG" initialAmount="0" metaid="iBioSim3"/>
-      <species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="aTc" initialAmount="0" metaid="iBioSim4"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="TetR" initialAmount="0" metaid="iBioSim5"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="GFP" initialAmount="0" metaid="iBioSim6"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P2" initialAmount="2" metaid="iBioSim7"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="C1" initialAmount="0" metaid="iBioSim8"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="C2" initialAmount="0" metaid="iBioSim9"/>
-      <species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="LacI" initialAmount="0" metaid="iBioSim10"/>
-    </listOfSpecies>
-    <listOfParameters>
-      <parameter constant="true" id="kd" metaid="iBioSim11" name="Degradation rate" value="0.0075"/>
-      <parameter constant="true" id="kc_f" metaid="iBioSim16" name="Forward complex formation rate" value="0.05"/>
-      <parameter constant="true" id="kc_r" metaid="iBioSim17" name="Reverse complex formation rate" value="1"/>
-      <parameter constant="true" id="nc" metaid="iBioSim18" name="Stoichiometry of binding" value="2"/>
-      <parameter constant="true" id="kr_f" metaid="iBioSim19" name="Forward repression binding rate" value="0.5"/>
-      <parameter constant="true" id="kr_r" metaid="iBioSim20" name="Reverse repression binding rate" value="1"/>
-      <parameter constant="true" id="ka_f" metaid="iBioSim21" name="Forward activation binding rate" value="0.0033"/>
-      <parameter constant="true" id="ka_r" metaid="iBioSim22" name="Reverse activation binding rate" value="1"/>
-      <parameter constant="true" id="ko_f" metaid="iBioSim23" name="Forward RNAP binding rate" value="0.033"/>
-      <parameter constant="true" id="ko_r" metaid="iBioSim24" name="Reverse RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kao_f" metaid="iBioSim25" name="Forward activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="kao_r" metaid="iBioSim26" name="Reverse activated RNAP binding rate" value="1"/>
-      <parameter constant="true" id="nr" metaid="iBioSim27" name="Initial RNAP count" value="30"/>
-      <parameter constant="true" id="ko" metaid="iBioSim28" name="Open complex production rate" value="0.05"/>
-      <parameter constant="true" id="kb" metaid="iBioSim29" name="Basal production rate" value="0.0001"/>
-      <parameter constant="true" id="ng" metaid="iBioSim30" name="Initial promoter count" value="2"/>
-      <parameter constant="true" id="np" metaid="iBioSim31" name="Stoichiometry of production" value="10"/>
-      <parameter constant="true" id="ka" metaid="iBioSim32" name="Activated production rate" value="0.25"/>
-    </listOfParameters>
-    <listOfReactions>
-      <reaction compartment="Cell" id="Degradation_TetR" metaid="iBioSim33" reversible="false" sboTerm="SBO:0000179">
-        <listOfReactants>
-          <speciesReference constant="true" species="TetR" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> TetR </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_GFP" metaid="iBioSim34" reversible="false" sboTerm="SBO:0000179">
-        <listOfReactants>
-          <speciesReference constant="true" species="GFP" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> GFP </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_C2" metaid="iBioSim35" reversible="false" sboTerm="SBO:0000179">
-        <listOfReactants>
-          <speciesReference constant="true" species="C2" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> C2 </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_LacI" metaid="iBioSim36" reversible="false" sboTerm="SBO:0000179">
-        <listOfReactants>
-          <speciesReference constant="true" species="LacI" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> LacI </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Degradation_C1" metaid="iBioSim37" reversible="false" sboTerm="SBO:0000179">
-        <listOfReactants>
-          <speciesReference constant="true" species="C1" stoichiometry="1"/>
-        </listOfReactants>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <times/>
-              <ci> kd </ci>
-              <ci> C1 </ci>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Complex_C1" metaid="iBioSim38" reversible="true" sboTerm="SBO:0000177">
-        <listOfReactants>
-          <speciesReference constant="true" species="IPTG" stoichiometry="1"/>
-          <speciesReference constant="true" species="LacI" stoichiometry="1"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference constant="true" species="C1" stoichiometry="1"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <minus/>
-              <apply>
-                <times/>
-                <apply>
-                  <times/>
-                  <ci> kc_f </ci>
-                  <apply>
-                    <power/>
-                    <ci> IPTG </ci>
-                    <ci> nc_IPTG </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <ci> LacI </ci>
-                  <ci> nc_LacI </ci>
-                </apply>
-              </apply>
-              <apply>
-                <times/>
-                <ci> kc_r </ci>
-                <ci> C1 </ci>
-              </apply>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="nc_IPTG" metaid="Complex_C1___nc_IPTG" name="nc_IPTG" value="1"/>
-            <localParameter id="nc_LacI" metaid="Complex_C1___nc_LacI" name="nc_LacI" value="1"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Complex_C2" metaid="iBioSim39" reversible="true" sboTerm="SBO:0000177">
-        <listOfReactants>
-          <speciesReference constant="true" species="aTc" stoichiometry="1"/>
-          <speciesReference constant="true" species="TetR" stoichiometry="1"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference constant="true" species="C2" stoichiometry="1"/>
-        </listOfProducts>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <minus/>
-              <apply>
-                <times/>
-                <apply>
-                  <times/>
-                  <ci> kc_f </ci>
-                  <apply>
-                    <power/>
-                    <ci> aTc </ci>
-                    <ci> nc_aTc </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <ci> TetR </ci>
-                  <ci> nc_TetR </ci>
-                </apply>
-              </apply>
-              <apply>
-                <times/>
-                <ci> kc_r </ci>
-                <ci> C2 </ci>
-              </apply>
-            </apply>
-          </math>
-                  <listOfLocalParameters>
-            <localParameter id="nc_aTc" metaid="Complex_C2___nc_aTc" name="nc_aTc" value="1"/>
-            <localParameter id="nc_TetR" metaid="Complex_C2___nc_TetR" name="nc_TetR" value="1"/>
-          </listOfLocalParameters>
-        </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P1" reversible="false" sboTerm="SBO:0000589">
-        <listOfProducts>
-          <speciesReference constant="true" species="GFP" stoichiometry="10"/>
-          <speciesReference constant="true" species="TetR" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="LacI"/>
-          <modifierSpeciesReference species="P1"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P1 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> LacI </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-      <reaction compartment="Cell" id="Production_P2" reversible="false">
-        <listOfProducts>
-          <speciesReference constant="true" species="LacI" stoichiometry="10"/>
-        </listOfProducts>
-        <listOfModifiers>
-          <modifierSpeciesReference species="P2"/>
-          <modifierSpeciesReference species="TetR"/>
-        </listOfModifiers>
-        <kineticLaw>
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <divide/>
-              <apply>
-                <times/>
-                <apply>
-                  <divide/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <times/>
-                      <ci> P2 </ci>
-                      <ci> ko </ci>
-                    </apply>
-                    <ci> ko_f </ci>
-                  </apply>
-                  <ci> ko_r </ci>
-                </apply>
-                <ci> nr </ci>
-              </apply>
-              <apply>
-                <plus/>
-                <apply>
-                  <plus/>
-                  <cn type="integer"> 1 </cn>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> ko_f </ci>
-                      <ci> ko_r </ci>
-                    </apply>
-                    <ci> nr </ci>
-                  </apply>
-                </apply>
-                <apply>
-                  <power/>
-                  <apply>
-                    <times/>
-                    <apply>
-                      <divide/>
-                      <ci> kr_f </ci>
-                      <ci> kr_r </ci>
-                    </apply>
-                    <ci> TetR </ci>
-                  </apply>
-                  <ci> nc </ci>
-                </apply>
-              </apply>
-            </apply>
-          </math>
-                </kineticLaw>
-      </reaction>
-    </listOfReactions>
-    <listOfEvents>
-      <event id="IPTG_high" metaid="iBioSim1" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 500 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="IPTG">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 60 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="IPTG_low" metaid="iBioSim12" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 1500 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="IPTG">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="aTc_high" metaid="iBioSim13" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 2000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="aTc">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 60 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-      <event id="aTc_low" metaid="iBioSim14" useValuesFromTriggerTime="false">
-        <trigger initialValue="false" persistent="false">
-          <math xmlns="http://www.w3.org/1998/Math/MathML">
-            <apply>
-              <geq/>
-              <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
-              <cn type="integer"> 3000 </cn>
-            </apply>
-          </math>
-                </trigger>
-        <listOfEventAssignments>
-          <eventAssignment variable="aTc">
-            <math xmlns="http://www.w3.org/1998/Math/MathML">
-              <cn type="integer"> 0 </cn>
-            </math>
-                    </eventAssignment>
-        </listOfEventAssignments>
-      </event>
-    </listOfEvents>
-  </model>
-</sbml>
diff --git a/GeneticCircuits/Toggle_Switch/RBA/jsbml.log b/GeneticCircuits/Toggle_Switch/RBA/jsbml.log
deleted file mode 100644
index 8bda126..0000000
--- a/GeneticCircuits/Toggle_Switch/RBA/jsbml.log
+++ /dev/null
@@ -1,107 +0,0 @@
-2023-02-02 12:08:21,958 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,960 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,960 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,962 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,963 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,963 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,966 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,966 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,966 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,967 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,967 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,967 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,968 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,968 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,968 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,969 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,969 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,969 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,970 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,970 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,970 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,971 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,971 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,971 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,972 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,972 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,972 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,973 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,973 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,973 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,974 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,974 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,974 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,974 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,974 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,975 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,975 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,975 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,975 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,976 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,976 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,976 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,977 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:08:21,977 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,977 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,978 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,978 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,978 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,978 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,979 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,979 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,979 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,979 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,979 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,980 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,981 WARN o.s.j.x.p.SBMLCoreParser [main] The element 'listOfLocalParameters' is not recognized.
-2023-02-02 12:08:21,981 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,981 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,981 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,982 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,982 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,982 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,983 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,983 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,983 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,984 ERROR o.s.j.x.p.SBMLCoreParser [main] Property compartment is not defined in reaction for Level 2 and Version 1.
-2023-02-02 12:08:21,985 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = compartment, value 'Cell' , element name = reaction
-2023-02-02 12:08:21,985 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'compartment' on the element reaction. Please check the specification for SBML.
-2023-02-02 12:08:21,985 ERROR o.s.j.x.p.SBMLCoreParser [main] Property constant is not defined in speciesReference for Level 2 and Version 1.
-2023-02-02 12:08:21,985 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = constant, value 'true' , element name = speciesReference
-2023-02-02 12:08:21,985 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'constant' on the element speciesReference. Please check the specification for SBML.
-2023-02-02 12:08:21,987 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1.
-2023-02-02 12:08:21,987 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:08:21,987 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:08:21,988 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,988 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:08:21,988 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:08:21,988 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,988 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:08:21,988 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:08:21,989 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1.
-2023-02-02 12:08:21,989 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:08:21,989 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:08:21,990 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,990 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:08:21,990 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:08:21,990 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,990 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:08:21,991 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:08:21,991 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1.
-2023-02-02 12:08:21,991 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:08:21,991 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:08:21,992 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,992 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:08:21,992 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:08:21,992 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,992 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:08:21,992 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:08:21,993 ERROR o.s.j.x.p.SBMLCoreParser [main] Property useValuesFromTriggerTime is not defined in event for Level 2 and Version 1.
-2023-02-02 12:08:21,993 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = useValuesFromTriggerTime, value 'false' , element name = event
-2023-02-02 12:08:21,994 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'useValuesFromTriggerTime' on the element event. Please check the specification for SBML.
-2023-02-02 12:08:21,994 ERROR o.s.j.x.p.SBMLCoreParser [main] Property initialValue is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,994 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = initialValue, value 'false' , element name = trigger
-2023-02-02 12:08:21,994 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'initialValue' on the element trigger. Please check the specification for SBML.
-2023-02-02 12:08:21,995 ERROR o.s.j.x.p.SBMLCoreParser [main] Property persistent is not defined in trigger for Level 2 and Version 1.
-2023-02-02 12:08:21,995 INFO o.s.j.x.p.SBMLCoreParser [main] Attribute = persistent, value 'false' , element name = trigger
-2023-02-02 12:08:21,995 WARN o.s.j.x.p.SBMLCoreParser [main] Could not recognize the attribute 'persistent' on the element trigger. Please check the specification for SBML.
diff --git a/GeneticCircuits/Toggle_Switch/README.md b/GeneticCircuits/Toggle_Switch/README.md
deleted file mode 100644
index 294a1e4..0000000
--- a/GeneticCircuits/Toggle_Switch/README.md
+++ /dev/null
@@ -1,7 +0,0 @@
-### Toggle Switch
-
-The toggle switch is a state holding gate and consists of two promoters each followed by a coding sequence. Each promoter is repressed by the protein transcribed by the other promoter [1].
-
-![Figure7](../../Media/ToggleSwitch.png)
-
-1. Gardner, T. S.; Cantor, C. R.; Collins, J. J. Construction of a Genetic Toggle Switch in Escherichia Coli. Nature 2000, 403 (6767), 339–342. https://doi.org/10.1038/35002131.
diff --git a/README.md b/README.md
index 889a631..c0ac7b8 100644
--- a/README.md
+++ b/README.md
@@ -16,6 +16,88 @@ Chemical reaction networks are systems including some number of chemical species
 
 Genetic circuits are part of synthetic biology, a research field combining engineering principles with biology. Researchers build circuits out of defined biological parts adding desired functionalities to biological systems. Automation in the design process allows scientists to model and analyze their genetic circuits \emph{in silico} to test the system before implementation. Stochastic model checking has been used to analyze genetic circuits before, which have an infinite state space and therefore suit the case studies presented here.
 
-### Fault Computing
+## Running STAMINA/Storm via Docker on Apple Silicon Mac
 
-Fault tolerant computing encompasses a wide variety of fault mechanisms and strategies to mitigate them. The case studies presented here focus on circuits that experience transient upsets modeled by Markov processes. Case studies in this field are given in two subcategories.
+This guide explains how to pull, configure, and run the `ifndefjosh/sstamina` tool using Docker on an Apple Silicon (M-series) Mac. It includes the specific configurations needed to bypass architecture mismatches, map local files, and call the exact internal binary path.
+
+### Prerequisites
+
+- [Docker Desktop](https://docker.com) installed and running on your computer.
+- Model files (e.g., `.sm` and `.props`) saved together in a dedicated project directory.
+
+---
+
+### Step-by-Step Instructions
+
+#### 1. Prepare Your Project Directory
+Before starting, ensure the terminal is inside the folder containing the model files. Docker uses the active folder to share files with the container.
+
+```bash
+cd /path/to/your/StaminaDocker
+```
+*(Verify your files are visible in this directory by running `ls` before proceeding).*
+
+#### 2. Download the Image
+Pull the verified `v3.0_2025` build from Docker Hub:
+
+```bash
+docker pull ifndefjosh/sstamina:v3.0_2025
+```
+
+#### 3. Run the Model Verification Command
+Because this container is built for Intel processors (`amd64`) and the internal tool path is not configured in the system `$PATH`, the tool must be executed using the absolute path while enabling Mac architecture emulation.
+
+Run the following command directly from the terminal (replace `your_model.prism` and `your_properties.csl` with the actual filenames):
+
+```bash
+docker run --rm \
+  --platform linux/amd64 \
+  -v "\$(pwd)":/data \
+  ifndefjosh/sstamina:v3.0_2025 \
+  /opt/stamina-storm/build/sstamina -J /data/your_model.prism /data/your_properties.csl
+```
+## Windows Alternatives
+
+If you are running the tool on Windows instead of macOS, you do not need the `--platform` flag, but you must adjust the folder mounting syntax depending on the shell environment:
+
+### Windows (PowerShell):
+```powershell
+docker run --rm \
+  -v "\${PWD}:/data" \
+  ifndefjosh/sstamina:v3.0_2025 \
+  /opt/stamina-storm/build/sstamina -J /data/your_model.prism /data/your_properties.csl
+```
+
+### Windows (Command Prompt - CMD):
+```cmd
+docker run --rm \
+  -v "%cd%:/data" \
+  ifndefjosh/sstamina:v3.0_2025 \
+  /opt/stamina-storm/build/sstamina -J /data/your_model.prism /data/your_properties.csl
+```
+
+---
+
+## Command Flag Breakdown
+
+- `--rm`: Automatically deletes the temporary container instance as soon as the calculation finishes to keep your system clean.
+- `--platform linux/amd64`: Forces the Apple Silicon Mac to use its internal translation layer (Rosetta/QEMU) to execute the Intel-based container code.
+- `-v "$(pwd)":/data`: Creates a live link between the current Mac folder (`$(pwd)`) and a virtual folder named `/data` inside the container.
+- `/opt/stamina-storm/build/sstamina`: Specifies the exact location of the compiled binary discovered inside this container version.
+- `/data/...`: Directs the tool to read the files from the shared virtual directory.
+
+---
+
+## Troubleshooting & Verification
+
+### Verifying File Sharing and Internal Paths
+If the tool reports that it cannot find the files, an interactive terminal can be opened directly inside the container to inspect the directories:
+
+```bash
+docker run --rm -it --platform linux/amd64 -v "\$(pwd)":/data ifndefjosh/sstamina:v3.0_2025 bash
+```
+
+Once inside the container terminal, these diagnostic checks can be run:
+- **Check files:** Type `ls /data` to confirm the Mac files are passing through successfully.
+- **Check the binary:** Type `ls /opt/stamina-storm/build` to verify the `sstamina` compilation file exists.
+- **Exit:** Type `exit` to return to the normal Mac terminal prompt.