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@sysbiomics Systems Biology at WV lab

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    14 repositories

    • Limosilactobacillus-fermentum-KUB-D18-GSMM

      Public
      genome-scale metabolic model of Limosilactobacillus fermentum KUB-D18
      MATLAB
      •0•0•0•0•Updated Feb 4, 2026Feb 4, 2026

    • sysmiome-serve

      Public
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated May 6, 2025May 6, 2025

    • SYSMIOME

      Public
      SYSMIOME toolbox.
      MIT License
      •0•0•0•0•Updated May 6, 2025May 6, 2025

    • vsearchpipeline

      Public
      VSEARCH pipeline for ASV inference of 16S seq data
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • libmiome

      Public
      Secondary pipeline
      Apache License 2.0
      •0•0•0•0•Updated Aug 13, 2024Aug 13, 2024

    • Cordyceps_militaris-tiGSMM

      Public
      MATLAB
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • itsbreeze

      Public
      ITS analysis pipeline written in nextflow
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 29, 2023Aug 29, 2023

    • minbreeze

      Public
      16s metabolic pipeline written in nextflow.
      R
      •
      MIT License
      •0•0•0•0•Updated Aug 29, 2023Aug 29, 2023

    • meta-gene

      Public
      The meta‐gene catalogue of Thai gut microbiome
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 9, 2022Sep 9, 2022

    • Cordyceps_militaris-GSMM

      Public
      The enhanced genome-scale metabolic model of Cordyceps militaris, iPC1469 through metabolic footprint and transcriptome profiles
      MATLAB
      •
      Creative Commons Attribution 4.0 International
      •0•0•1•0•Updated Jul 12, 2022Jul 12, 2022

    • Limosilactobacillus_reuteri_KUB_AC5-GSMM

      Public
      A high quality genome-scale metabolic model of probiotic L. reuteri KUB-AC5
      MATLAB
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 7, 2022Feb 7, 2022

    • nxf-kraken2

      Public
      A simple nextflow pipeline for running kraken2 and bracken in a docker container
      Groovy
      •
      MIT License
      •8•0•0•0•Updated Aug 12, 2021Aug 12, 2021

    • Cordyceps_militaris-GEM

      Public
      Genome-scale metabolic model of Cordyceps militaris
      metabolic-engineeringgenome-scale-models
      metabolic-engineeringgenome-scale-models
      MATLAB
      •
      Creative Commons Attribution 4.0 International
      •2•2•0•0•Updated Apr 19, 2020Apr 19, 2020

    • aspergillus_model

      Public
      Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae
      metabolic-networkflux-balance-analysismetabolic-model
      metabolic-networkflux-balance-analysismetabolic-modelreconstructed-metabolic-networkaspergillus-oryzae
      MATLAB
      •
      MIT License
      •0•2•0•0•Updated Mar 29, 2019Mar 29, 2019
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