NEURON tools and utilites for NeuroML
Cerebellum model generated using
Tools for Using NeuroML with NEURON
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
- Import of NeuroML morphologies into NEURON*
Files to allow import of NeuroML Level 1 & 2 compliant cell morphologies into
NEURON are available here.
- Conversion of ChannelML at the command line
A Python based utility
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.
- 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.
NOTE: Much of this functionality has been reproduced/improved on in jNeuroML
which can import SBML & export in NEURON (and other formats).
Versions of these files have been present in NEURON from version 6.0, but the latest will continue
be available from this site.