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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.

Development

After cloning, run once:

make bootstrap

This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.

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

About

An application for fitting systems biology models using metaheuristic algorithms

Resources

Readme
License

Contributing

Contributing
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GitHub - dynova/PyBNF: An application for fitting systems biology models using metaheuristic algorithms · GitHub
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alt text
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.
Development
After cloning, run once:
make bootstrap
This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.
PyBioNetFit is released under the BSD-3 license. For more information, refer to the
LICENSE. LANL code designation: C18062
About
An application for fitting systems biology models using metaheuristic algorithms
Resources
Readme
License
Contributing
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GitHub - dynova/PyBNF: An application for fitting systems biology models using metaheuristic algorithms · GitHub
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alt text
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.
Development
After cloning, run once:
make bootstrap
This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.
PyBioNetFit is released under the BSD-3 license. For more information, refer to the
LICENSE. LANL code designation: C18062
About
An application for fitting systems biology models using metaheuristic algorithms
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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var __re = new RegExp('^' + ".*" + '
GitHub - dynova/PyBNF: An application for fitting systems biology models using metaheuristic algorithms · GitHub
Skip to content
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alt text
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.
Development
After cloning, run once:
make bootstrap
This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.
PyBioNetFit is released under the BSD-3 license. For more information, refer to the
LICENSE. LANL code designation: C18062
About
An application for fitting systems biology models using metaheuristic algorithms
Resources
Readme
License
Contributing
Contributing
Activity
Stars
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0 watching
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0 forks
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GitHub - dynova/PyBNF: An application for fitting systems biology models using metaheuristic algorithms · GitHub
Skip to content
BranchesTags
Repository files navigation
alt text
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.
Development
After cloning, run once:
make bootstrap
This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.
PyBioNetFit is released under the BSD-3 license. For more information, refer to the
LICENSE. LANL code designation: C18062
About
An application for fitting systems biology models using metaheuristic algorithms
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, 'i');
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - dynova/PyBNF: An application for fitting systems biology models using metaheuristic algorithms · GitHub
Skip to content
BranchesTags
Repository files navigation
alt text
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.
Development
After cloning, run once:
make bootstrap
This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.
PyBioNetFit is released under the BSD-3 license. For more information, refer to the
LICENSE. LANL code designation: C18062
About
An application for fitting systems biology models using metaheuristic algorithms
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, 'i');
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var __re = new RegExp('^' + ".*" + '
GitHub - dynova/PyBNF: An application for fitting systems biology models using metaheuristic algorithms · GitHub
Skip to content
BranchesTags
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alt text
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.
Development
After cloning, run once:
make bootstrap
This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.
PyBioNetFit is released under the BSD-3 license. For more information, refer to the
LICENSE. LANL code designation: C18062
About
An application for fitting systems biology models using metaheuristic algorithms
Resources
Readme
License
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, 'i');
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console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
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}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
GitHub - dynova/PyBNF: An application for fitting systems biology models using metaheuristic algorithms · GitHub
Skip to content
BranchesTags
Repository files navigation
alt text
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.
Development
After cloning, run once:
make bootstrap
This installs the pre-push git hook (via pre-commit) so the bngsim test subset runs locally before any git push.
PyBioNetFit is released under the BSD-3 license. For more information, refer to the
LICENSE. LANL code designation: C18062
About
An application for fitting systems biology models using metaheuristic algorithms
Resources
Readme
License
Contributing
Contributing
Activity
Stars
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Watchers
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Forks
0 forks
Report repository
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