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Padraig Gleeson, 30 Apr 2014 14:57
C elegans muscle cell model in NeuroML 2¶
This introduction is currently only for the NeuroML 2 implementation of the C elegans muscle cell model of Boyle & Cohen.
For more details see the README/wiki on the GitHub site: https://github.com/openworm/muscle\_model
Cloning the repository¶
Get a local copy of the repository with:
git clone https://github.com/openworm/muscle_model.git
or
git clone git
github.com:openworm/muscle_model.git@
if you have SSH authentication set up (see here).
Run the NeuroML 2 example¶
Install the Java parser simulator for NeuroML 2 (currently called libNeuroML, see here). Remember to set the NML2_HOME environment variable.
Go in to the directory with the NeuroML 2 version of the model:
cd muscle_model/NeuroML2
Run the example cell (trying to reproduce Figure 2A in Boyle & Cohen 2008) with:
nml2 Figure2A.xml
Run the example cell (trying to reproduce Figure 2B in Boyle & Cohen 2008) with:
nml2 Figure2B.xml