BioSimulators-BioNetGen documentation

BioSimulators-BioNetGen provides a BioSimulators-compliant command-line interface to the BioNetGen biological simulation tool. A Docker image for this package is also available.

This command-line interface and Docker image enable users to use BioNetGen to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in BNGL format).

A list of the algorithms and algorithm parameters supported by BioNetGen is available at BioSimulators.

A simple web application and web service for using BioNetGen to execute COMBINE/OMEX archives is also available at runBioSimulations.

Contents

• Installation instructions
  • Command-line program
  • Docker image with a command-line entrypoint
• Tutorial
  • Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML
  • Command-line program
  • Docker image with a command-line entrypoint
• API documentation
  • Submodules
  • biosimulators_bionetgen.config module
  • biosimulators_bionetgen.core module
  • biosimulators_bionetgen.data_model module
  • biosimulators_bionetgen.io module
  • biosimulators_bionetgen.utils module
  • biosimulators_bionetgen.warnings module
• About BioSimulators-BioNetGen
  • License
  • Development team
  • Questions and comments
• Index