c302

c302

The c302 framework is in the process of moving here from https://github.com/openworm/CElegansNeuroML/tree/master/CElegans/pythonScripts/c302

c302 is a framework for generating network models in NeuroML 2 based on C elegans connectivity data.

c302 structure

It uses information on the synaptic connectivity of the network (from
here) and uses
libNeuroML to generate
a network in valid NeuroML, which can be run in jNeuroML or pyNeuroML.

To install & test

The full set of dependencies for c302 can be installed with the following (see also the Travis-CI script):

python setup.py install

To regenerate a set of NeuroML & LEMS files for one instance of the model and execute it:

python c302/c302_Full.py                         # To regenerate the NeuroML & LEMS files
pynml examples/LEMS_c302_A_Full.xml         # Run a simulation with jNeuroML via pyNeuroML

To test all of the working features of the framework run test.sh:

./test.sh

Command line interface

This package can be used to generate customised networks of varying size, with different cells stimulated, of varying duration from the command line:

./c302/__init__.py MyNetwork parameters_A -cells ["ADAL","AIBL","RIVR","RMEV"] -cellstostimulate ["ADAL","RIVR"] -duration 500

This will create a NeuroML 2 file and a LEMS file to execute it, containing 4 cells, stimulating 2 of them, and with a duration of 500 ms

More options can be found with

./c302/__init__.py -h

Mapping to NEURON

Due to the fact that the cells are in pure NeuroML2, they can be mapped to other formats using the export feature of jNeuroML. Install NEURON and map the network to this format using:

cd examples

for jNeuroML:

jnml LEMS_c302_A_Pharyngeal.xml -neuron

or instead for pyNeuroML:

pynml LEMS_c302_A_Pharyngeal.xml -neuron

then

nrnivmodl
nrngui -python LEMS_c302_A_Pharyngeal_nrn.py

Comparing activity across scales/parameter sets

activity

See here for more details on this.

Understanding how c302_Full.py works

Build Status

Under active development. See https://github.com/openworm/c302/issues

Developer: Stephen Larson

Scientific Coordinator: Padraig Gleeson

This model was originally developed in: NeuroML2

The code for this model is hosted on GitHub: https://github.com/openworm/c302.git

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