C. elegans models in NeuroML and neuroConstruct
NOTE: There is a new initiative which uses Python scripts to generate network models in NeuroML2 at multiple levels of detail: c302. This has been moved to its own repository, and replaces much of the functionalty here!
This repository contains a neuroConstruct (http://www.neuroConstruct.org) project containing a model of the C. elegans nervous system, see here.
The NeuroML files are available under the directories generatedNeuroML, and generatedNeuroML2.
This is being developed as part of the OpenWorm project.
Installation
python setup.py install
Data on which this model is based
The C. elegans 3D model this was derived from was produced by Dr. Christian Grove and Dr. Paul Sternberg at the VirtualWorm project (WormBase, CalTech) and released into the public domain. You can visit the VirtualWorm home page at http://caltech.wormbase.org/virtualworm/
We have converted all 302 neurons described in the WormBase Virtual Worm Blender files. We have represented them as multi-compartmental neuronal models. This captures the positions of the cells in context with each other and gives us a place to start building descriptions of the synaptic junctions and the ion channels for each cell. In addition, we have added details of connectivity between neurons into the neuroConstruct project.
Important Limitations
Please note:
- An accurate representation of the ion channels and their distributions in each neuron has not yet been attempted. Work on a cell model from C. elegans with ion channels can be found here
- An accurate representation of the synapses between the neurons has not yet been attempted. They are simplistic synapses only for the moment.
More accurate models of conductance based neurons and more realistic synapses will be incorporated into c302 first, and then the neuroConstruct model will be updated.
Running the neuroConstruct model
For full details on running this neuroConstruct project see: https://github.com/openworm/OpenWorm/wiki/Running-the-C.-elegans-model-in-neuroConstruct.
