https://github.com/lanl/pybnf

An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.
https://github.com/lanl/pybnf

Last synced: about 1 year ago
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An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.

• Host: GitHub
• URL: https://github.com/lanl/pybnf
• Owner: lanl
• License: other
• Created: 2018-03-19T02:23:27.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2023-12-13T22:00:54.000Z (over 2 years ago)
• Last Synced: 2025-04-12T11:08:17.222Z (about 1 year ago)
• Language: Python
• Homepage:
• Size: 115 MB
• Stars: 24
• Watchers: 5
• Forks: 18
• Open Issues: 48
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
![alt text](docs/Logo1.png "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, 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](Documentation_PyBioNetFit.pdf) or the online documentation at .

PyBioNetFit is released under the BSD-3 license. For more information, refer to the

[LICENSE](LICENSE). LANL code designation: C18062