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, 2008.

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 gitgithub.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

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:

simplified Figure1A