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Padraig Gleeson, 03 Jun 2014 10:18
C elegans muscle cell model in NeuroML 2¶
This introduction is currently for the NeuroML 2 implementation of the C elegans muscle cell model of Boyle & Cohen, 2008 and also for the simplified (pure Hodgkin Huxley) model.
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 latest binary for jNeuroML (see here), or install & build the development version of jNeuroML. Remember to set the JNML_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:
jnml LEMS_Figure2A.xml
Run the example cell (trying to reproduce Figure 2B in Boyle & Cohen, 2008) with:
jnml LEMS_Figure2B.xml
Simplified model¶
There is also a simplified muscle cell model which Mike Vella is building from scratch with Alexander Dibert in the Pyramidal framework, here is a sample trace, it is currently in the calcium_experiments branch of the github repository.