Wiki » History » Version 9
Mike Vella, 30 Apr 2014 14:57
1 | 1 | Padraig Gleeson | C elegans muscle cell model in NeuroML 2 |
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2 | 1 | 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 | 1 | Padraig Gleeson | Cloning the repository |
9 | 1 | Padraig Gleeson | ---------------------- |
10 | 1 | Padraig Gleeson | |
11 | 1 | Padraig Gleeson | Get a local copy of the repository with: |
12 | 1 | Padraig Gleeson | |
13 | 1 | Padraig Gleeson | `git clone https://github.com/openworm/muscle_model.git` |
14 | 1 | Padraig Gleeson | |
15 | 1 | Padraig Gleeson | or |
16 | 1 | Padraig Gleeson | |
17 | 1 | Padraig Gleeson | `git clone git`github.com:openworm/muscle\_model.git@ |
18 | 1 | Padraig Gleeson | |
19 | 1 | Padraig Gleeson | if you have SSH authentication set up (see [here](https://help.github.com/articles/set-up-git)). |
20 | 1 | Padraig Gleeson | |
21 | 1 | Padraig Gleeson | Run the NeuroML 2 example |
22 | 1 | Padraig Gleeson | ------------------------- |
23 | 1 | Padraig Gleeson | |
24 | 1 | Padraig Gleeson | Install the Java parser simulator for NeuroML 2 (currently called libNeuroML, see [here](http://www.neuroml.org/neuroml2.php#libNeuroML)). Remember to set the **NML2\_HOME** environment variable. |
25 | 1 | Padraig Gleeson | |
26 | 1 | Padraig Gleeson | Go in to the directory with the NeuroML 2 version of the model: |
27 | 1 | Padraig Gleeson | |
28 | 1 | Padraig Gleeson | `cd muscle_model/NeuroML2` |
29 | 1 | Padraig Gleeson | |
30 | 5 | Padraig Gleeson | Run the example cell (trying to reproduce Figure 2A in [Boyle & Cohen, 2008](http://www.sciencedirect.com/science/article/pii/S0303264708001408)) with: |
31 | 1 | Padraig Gleeson | |
32 | 3 | Padraig Gleeson | `nml2 Figure2A.xml` |
33 | 1 | Padraig Gleeson | |
34 | 1 | Padraig Gleeson | ![](http://www.opensourcebrain.org/attachments/download/35/Selection_096.png) |
35 | 3 | Padraig Gleeson | |
36 | 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: |
37 | 3 | Padraig Gleeson | |
38 | 3 | Padraig Gleeson | `nml2 Figure2B.xml` |
39 | 3 | Padraig Gleeson | |
40 | 4 | Padraig Gleeson | ![](http://www.opensourcebrain.org/attachments/download/36/Selection_098.png) |
41 | 1 | Padraig Gleeson | |
42 | 9 | Mike Vella | Simplified model |
43 | 9 | Mike Vella | ---------------- |
44 | 9 | Mike Vella | |
45 | 9 | Mike Vella | 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. |
46 | 7 | Mike Vella | |
47 | 7 | Mike Vella | `simplified Figure1A` |
48 | 7 | Mike Vella | |
49 | 8 | Mike Vella | ![](http://www.opensourcebrain.org/attachments/download/37/simplified.png) |