BioSimulators-GillesPy2 documentation

BioSimulators-GillesPy2 provides a BioSimulators-compliant command-line interface to the GillesPy2 biological simulation tool. A Docker image for this package is also available.

This command-line interface and Docker image enable users to use GillesPy2 to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in SBML format).

A list of the algorithms and algorithm parameters supported by GillesPy2 is available at BioSimulators.

A simple web application and web service for using GillesPy2 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_gillespy2.core module
  • biosimulators_gillespy2.data_model module
• About BioSimulators-GillesPy2
  • License
  • Development team
  • Questions and comments
• Index