biosimulators-test-suite 0.1.88

Tools for validating that biosimulation tools are consistent with the BioSimulators standards

BioSimulators test suite

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.

Installation instructions, tutorial, and API documentation

Installation instructions, tutorial, and API documentation are available here.

License

The software in this package is released under the MIT License. The modeling projects in this package are released under the Creative Commons 1.0 Universal (CC0) license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, the https://health.uconn.edu/cell-analysis-modeling/ at the University of Connecticut, and the Center for Reproducible Biomedical Modeling with assistance from the contributors listed here.

Contributing to the test suite

We enthusiastically welcome contributions to the test suite! Please see the guide to contributing and the developer’s code of conduct.

Acknowledgements

This work was supported by National Institutes of Health award P41EB023912.

Questions and comments

Please contact the BioSimulators Team with any questions or comments.