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 `git clone https://github.com/openworm/muscle\_model.git https://github.com/openworm/muscle_model.git`

or

git `git clone git@github.com:openworm/muscle\_model.git 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 Java parser simulator for jNeuroML (see [here](https://github.com/NeuroML/jNeuroML/blob/master/README.md)). NeuroML 2 (currently called libNeuroML, see [here](http://www.neuroml.org/neuroml2.php#libNeuroML)). Remember to set the **JNML\_HOME** **NML2\_HOME** environment variable.

Go in to the directory with the NeuroML 2 version of the model:

cd muscle\_model/NeuroML2 `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 `nml2 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 `nml2 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`