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github:NeuroML2/README.md
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 binary for jNeuroML (see [here](https://github.com/NeuroML/jNeuroML/blob/master/README.md)), or install & build the **development version** of jNeuroML. 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
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
### 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](https://github.com/openworm/muscle_model/tree/calcium_experiments) of the github repository.
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 latest binary for jNeuroML (see [here](https://github.com/NeuroML/jNeuroML/blob/master/README.md)), or install & build the **development version** of jNeuroML. 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
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
### 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](https://github.com/openworm/muscle_model/tree/calcium_experiments) of the github repository.
