Neuron Tools And Utilities For NeuroML

Cerebellum model generated using neuroConstruct.

The links below can be used to view latest versions of the associated code as well as the revision history, or all of the code (including the NetBeans project containing the specification tree and validation application) can be checked out of the Subversion repository as outlined here.

  • Export of NeuroML cells from NEURON's ModelView*
    Files to allow export of NeuroML Level 1 & 2 compliant cell morphologies from ModelView in NEURON are available here (README).

  • Import of NeuroML morphologies into NEURON*
    Files to allow import of NeuroML Level 1 & 2 compliant cell morphologies into NEURON are available here (README).

  • Conversion of ChannelML at the command line
    A Python based utility here can be used to convert ChannelML files to NEURON mod files at the command line. (Note that this can easily be altered to convert ChannelML to GENESIS or PSICS scripts.) An optional flag -modc will also compile the generated mod files in one command.

    A better alternative to the tool below for converting SBML to LEMS and from there to NEURON is to use the import & export features of jNeuroML.

  • Conversion of SBML files for use in NEURON
    A **PROVISIONAL** implementation of an SBML to NEURON converter is available here (README). This uses the Python bindings of libSBML to generate a mod file containing the model represented in a simple SBML file, which can then be inserted onto a section in NEURON for simulation. Note that only a restricted set of SBML elements are supported, but it can be used to simulate some of the models in the BioModels database, as illustrated below. This is a work in progress and will be developed further to allow closer integration between NeuroML & SBML in realistic neuronal models.


*Versions of these files have been present in NEURON from version 6.0, but the latest will continue be available from this site.
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