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](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 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 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 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`