BioSimulators test suite documentation

The BioSimulators test suite is a tool for validating that biosimulation software tools implement the BioSimulators conventions for biosimulation tools.

The test suite is composed of two parts:

• A collection of example modeling projects. Each project is represented by a single COMBINE/OMEX archive that contains one or more simulation experiments described using the Simulation Experiment Description Markup Language (SED-ML) and one or more models described using a format such as the BioNetGen Language (BNGL)) or the Systems Biology Markup Language (SBML).

• Software for checking that biosimulation tools execute these projects according to the BioSimulators conventions.

  • Simulation tools support the BioSimulators standard command-line arguments.

  • Simulation tools support the BioSimulators conventions for Docker images.

  • Simulation tools follow the BioSimulators conventions for executing simulations described by SED-ML files in COMBINE/OMEX archives.

  • Simulation tools support the BioSimulators conventions for the outputs of SED-ML files in COMBINE/OMEX archives.

Contents

• Installation instructions
  • Install the dependencies for the test suite
  • Install the optional dependencies for the test suite
  • Install the test suite
• Tutorial
  • Using the public cloud deployment of the test suite
  • Running the test suite locally
• API documentation
  • Subpackages
  • Submodules
  • biosimulators_test_suite.config module
  • biosimulators_test_suite.data_model module
  • biosimulators_test_suite.exceptions module
  • biosimulators_test_suite.exec_cli module
  • biosimulators_test_suite.exec_core module
  • biosimulators_test_suite.exec_gh_action module
  • biosimulators_test_suite.utils module
  • biosimulators_test_suite.warnings module
• About the BioSimulators test suite
  • License
  • Development team
  • Contributing to the BioSimulators test suite
  • Acknowledgements
  • Questions and comments
• Index