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 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
git clone gitgithub.com:openworm/muscle_model.git@
if you have SSH authentication set up (see here).
Run the NeuroML 2 example¶
Install the Java parser simulator for NeuroML 2 (currently called libNeuroML, see here). Remember to set the NML2_HOME environment variable.
Go in to the directory with the NeuroML 2 version of the model:
Run the example cell (trying to reproduce Figure 2A in Boyle & Cohen, 2008) with:
Run the example cell (trying to reproduce Figure 2B in Boyle & Cohen, 2008) with:
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.