Wiki » History » Version 15
Padraig Gleeson, 03 Jun 2014 10:18
1 | 1 | Padraig Gleeson | C elegans muscle cell model in NeuroML 2 |
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2 | 10 | Padraig Gleeson | ---------------------------------------- |
3 | 1 | Padraig Gleeson | |
4 | 9 | Mike Vella | 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. |
5 | 1 | Padraig Gleeson | |
6 | 1 | Padraig Gleeson | For more details see the README/wiki on the GitHub site: https://github.com/openworm/muscle\_model |
7 | 1 | Padraig Gleeson | |
8 | 10 | Padraig Gleeson | ### Cloning the repository |
9 | 1 | Padraig Gleeson | |
10 | 1 | Padraig Gleeson | Get a local copy of the repository with: |
11 | 1 | Padraig Gleeson | |
12 | 13 | Padraig Gleeson | git clone https://github.com/openworm/muscle\_model.git |
13 | 1 | Padraig Gleeson | |
14 | 1 | Padraig Gleeson | or |
15 | 1 | Padraig Gleeson | |
16 | 13 | Padraig Gleeson | git clone git@github.com:openworm/muscle\_model.git |
17 | 1 | Padraig Gleeson | |
18 | 1 | Padraig Gleeson | if you have SSH authentication set up (see [here](https://help.github.com/articles/set-up-git)). |
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20 | 11 | Padraig Gleeson | ### Run the NeuroML 2 example |
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22 | 14 | Padraig Gleeson | 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. |
23 | 1 | Padraig Gleeson | |
24 | 1 | Padraig Gleeson | Go in to the directory with the NeuroML 2 version of the model: |
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26 | 13 | Padraig Gleeson | cd muscle\_model/NeuroML2 |
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28 | 1 | Padraig Gleeson | Run the example cell (trying to reproduce Figure 2A in [Boyle & Cohen, 2008](http://www.sciencedirect.com/science/article/pii/S0303264708001408)) with: |
29 | 1 | Padraig Gleeson | |
30 | 13 | Padraig Gleeson | jnml LEMS_Figure2A.xml |
31 | 1 | Padraig Gleeson | |
32 | 14 | Padraig Gleeson | ![](http://www.opensourcebrain.org/attachments/download/201/Selection_079.png) |
33 | 3 | Padraig Gleeson | |
34 | 5 | Padraig Gleeson | Run the example cell (trying to reproduce Figure 2B in [Boyle & Cohen, 2008](http://www.sciencedirect.com/science/article/pii/S0303264708001408)) with: |
35 | 3 | Padraig Gleeson | |
36 | 14 | Padraig Gleeson | jnml LEMS_Figure2B.xml |
37 | 3 | Padraig Gleeson | |
38 | 15 | Padraig Gleeson | ![](http://opensourcebrain.org/attachments/download/202/Selection_080.png) |
39 | 9 | Mike Vella | |
40 | 9 | Mike Vella | ### Simplified model |
41 | 7 | Mike Vella | |
42 | 15 | Padraig Gleeson | 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. |
43 | 7 | Mike Vella | |
44 | 8 | Mike Vella | ![](http://www.opensourcebrain.org/attachments/download/37/simplified.png) |