C elegans muscle cell model in NeuroML 2

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This introduction is currently for the NeuroML 2 implementation of the C elegans muscle cell model of [Boyle & Cohen, 2008](http://www.sciencedirect.com/science/article/pii/S0303264708001408) 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](https://help.github.com/articles/set-up-git)).



### Run the NeuroML 2 example



Install the latest latets binary for jNeuroML (see [here](https://github.com/NeuroML/jNeuroML/blob/master/README.md)). 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](http://www.sciencedirect.com/science/article/pii/S0303264708001408)) with:



jnml LEMS_Figure2A.xml


Figure2A.xml


Run the example cell (trying to reproduce Figure 2B in [Boyle & Cohen, 2008](http://www.sciencedirect.com/science/article/pii/S0303264708001408)) with:



jnml LEMS_Figure2B.xml

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.



`simplified Figure1A`