PyBioNetFit (PyBNF) is a general-purpose program for parameterizing biological models specified using the BioNetGen rule-based modeling language (BNGL) or the Systems Biology Markup Language (SBML). PyBioNetFit offers a suite of parallelized metaheuristic algorithms (differential evolution, particle swarm optimization, scatter search) for parameter optimization. In addition to model parameterization, PyBNF supports uncertainty quantification by bootstrapping or Bayesian approaches, and model checking. PyBNF includes an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm, which supports Bayesian inference. PyBNF includes the Biological Property Specification Language (BPSL) for defining qualitative data for use in parameterization or checking. It runs on most Linux and macOS workstations as well on computing clusters.

For documentation, refer to Documentation_PyBioNetFit.pdf or the online documentation at https://pybnf.readthedocs.io/en/latest/.

Installation

PyBNF requires Python 3.10 or higher.

python3 -m pip install pybnf

With uv, PyBNF can also be installed as a command-line tool:

uv tool install pybnf

PyBNF installs its Python dependencies, including BNGsim and libRoadRunner, through the package metadata. BNGL workflows can still require a BioNetGen installation for BNG2.pl; see the installation documentation for simulator setup details.

PyBioNetFit is released under the BSD-3 license. For more information, refer to the LICENSE. LANL code designation: C18062