PyBioNetFit

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, PyBioNetFit supports uncertainty quantification by bootstrapping and Bayesian approaches, and model checking. PyBioNetFit 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.

Documentation

PyBioNetFit documentation is available online at readthedocs or for download in PDF format.

Installation

PyBioNetFit is installed with the pip Python package manager with the command

pip install pybnf

More information is available in the relevant section of the documentation. PyBioNetFit can also be installed from source code available on GitHub.

Support and Feedback

The PyBioNetFit developers can be contacted through GitHub.