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CElegansNeuroML

NeuroML based C elegans model, contained in a neuroConstruct project, as well as c302

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Statistics on CElegansNeuroML

Number of watchers on Github 95
Number of open issues 38
Average time to close an issue 4 months
Main language XSLT
Average time to merge a PR 6 days
Open pull requests 8+
Closed pull requests 4+
Last commit over 1 year ago
Repo Created about 7 years ago
Repo Last Updated over 1 year ago
Size 237 MB
Homepage http://opensource...
Organization / Authoropenworm
Contributors8
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C. elegans models in NeuroML and neuroConstruct

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.

There is also a new initiative which uses Python scripts to generate network models in NeuroML2 at multiple levels of details: c302. This will eventually be fully integrated with the neuroConstruct version.

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.

Build Status

CElegansNeuroML open issues Ask a question     (View All Issues)
  • over 2 years Implement parameters D
  • over 2 years Running OpenWorm simulations on SpiNNaker
  • almost 3 years What would it take to replay a specific pattern of activity into certain c302 neurons during a simulation run?
  • almost 3 years Can c302 with jNeuroML-NEURON take advantage of multiple CPU cores?
  • almost 3 years What would it take to include activity dependent conductances?
  • over 3 years Make OpenSourceBrain's visualization of this repo include Hive Plots
  • over 3 years Make it easier to get at simulation results
  • almost 4 years Test python scripts
  • almost 4 years Ensure consistent directory structure and naming schemes for tests
  • almost 4 years Check for performance regressions in testing suite
  • almost 4 years Create tests to catch performance regressions in specific functions
  • about 4 years Full implementation in WormSim
  • about 4 years Design WormSim UI additions for the muscle neuron model
  • about 4 years Run/visualize motor neuron network in Geppetto
  • about 4 years Run multi-scale optimization for motor neuron network
  • about 4 years Create a multi-level optimization scaffold that tunes motor neuron network parameters to fit within physiological bounds
  • about 4 years Create appropriate tests to constrain motor neuron network parameters within physiological bounds
  • about 4 years Construct target quantitative/qualitative electrophysiological behaviour
  • about 4 years Verify that the neurons, channels and parameters for this subnetwork are visible in the model completion dashboard
  • about 4 years Create validation tests for all gap junctions between key motor neurons
  • about 4 years Create validation tests for all synapses between key motor neurons
  • about 4 years Embed best-guess ion channels in motor/neuron cell models
  • about 4 years Make a best guess for ion channels in relevant cells
  • about 4 years Document the tests in c302
  • about 4 years Validate two tests of c302 connectivity using SciUnit
  • about 4 years Run tests using the pytest framework rather than standard unittests
  • about 4 years Run c302 README examples in doctests
  • about 4 years Make sure there are examples in the README for key functions of c302
  • about 4 years Change data source to PyOpenWorm in unit tests
  • about 4 years Adapt current data loading process in c302.py to pull data from PyOpenWorm
CElegansNeuroML open pull requests (View All Pulls)
  • adding CompareMain.py
  • Attempt to match named cells in Kato paper
  • Separation of generic synapse into neuron-to-neuron and neuron-to-muscle synapses on all levels.
  • Add config params to override
  • Updates for OpenWorm 0.7 release
  • Optimizer improvements
  • 2to3
  • Making c302 more module like
CElegansNeuroML list of languages used
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