C elegans muscle cell model in NeuroML 2¶

This is a NeuroML 2 implementation of the C elegans muscle cell model of Boyle & Cohen, 2008.

To install & run this version, install either jNeuroML (for jnml, as outlined here), or PyNeuroML (for pynml, as outlined here).

Get a local copy of this repository with:

git clone https://github.com/openworm/muscle_model.git

or

git clone git@github.com:openworm/muscle_model.git  # if SSH authentication is set up locally

Go into 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  # using jNeuroML

or

pynml LEMS_Figure2A.xml  # using PyNeuroML

Run the example cell (trying to reproduce Figure 2B in Boyle & Cohen, 2008) with:

jnml LEMS_Figure2B.xml
pynml LEMS_Figure2B.xml

An iPython notebook with examples of how to explore elements of the muscle model is available at Explore.ipynb.

For more details on the current status of this conversion, see issue: https://github.com/openworm/OpenWorm/issues/169

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.