BioSimulators-AMICI documentation

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

This command-line interface and Docker image enable users to use AMICI 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 AMICI is available at BioSimulators.

A simple web application and web service for using AMICI 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
  • exec_sed_doc()
  • exec_sed_task()
  • exec_sedml_docs_in_combine_archive()
  • get_simulator_version()
  • preprocess_sed_task()
  • Submodules
  • biosimulators_amici.core module
  • biosimulators_amici.data_model module
• About BioSimulators-AMICI
  • License
  • Development team
  • Questions and comments
• Index