BioSimulators-pyNeuroML documentation

BioSimulators-pyNeuroML provides BioSimulators-compliant command-line interfaces for the jNeuroML / pyNeuroML, NetPyNE, and NEURON biological simulation tools. Docker images for these package are also available.

These command-line interfaces and Docker images enable users to use jNeuroML/pyNeuroML, NetPyNe, and NEURON to execute COMBINE/OMEX archives that describe one or more simulation experiments (in SED-ML format) of one or more models (in NeuroML / LEMS format).

A list of the algorithms and algorithm parameters supported by jNeuroML/pyNeuroML, NetPyNe, and NEURON is available at BioSimulators.

A simple web application and web service for using jNeuroML/pyNeuroML, NetPyNe, and NEURON to execute COMBINE/OMEX archives is also available at runBioSimulations.

Contents

• Installation instructions
  • Command-line program
  • Docker images with command-line entrypoints
• Tutorial
  • Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML
  • Command-line program
  • Docker images with command-line entrypoints
• API documentation
  • Subpackages
  • Submodules
  • biosimulators_pyneuroml.core module
  • biosimulators_pyneuroml.data_model module
  • biosimulators_pyneuroml.utils module
• About BioSimulators-pyNeuroML
  • License
  • Development team
  • Questions and comments
• Index