Open Worm muscle model

Authors: Mike Vella, Alex Dibert, Padraig Gleeson email:mv333@cam.ac.uk

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Introduction

This repository contains the following:

1. Simulation of C.Elegans muscle cell electrical properties, based on Boyle & Cohen 2008.

2. Optimization script for the above model, utliising Optimal Neuron package. Optimizing towards sharp electrode data obtained from lab of Michael M Francis.

3. C++ Module for importation of arbitrary Pyramidal model into C++ program such as Palyanov et al SPH solver.

4. NeuroML 2/LEMS conversion of the muscle cell model

5. Simulation of C.Elegans muscle cell electrical properties

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2. Optimization script for the above model

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Note: see openworm#18 for details on the current status of these subprojects.

See https://github.com/openworm/muscle_model/blob/master/pyramidal_implementation/README.md

3. C++ Module for SPH/muscle_model integration

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Note: see openworm#18 for details on the current status of these subprojects.

This is still at an alpha stage, but has been demonstrated to function as expected.

to compile and run (temp notes with hardcoded paths - replace with your own path) run the following commands from inside curdir:

$ export PYTHONPATH="/home/mike/dev/cpp_pyramidal_integration/" OR export PYTHONPATH=$PYTHONPATH:/home/mike/dev/muscle_model/pyramidal_implementation/ $ g++ main.cpp -l python2.7 -o sim -I /usr/include/python2.7/ $ ./sim

The resultant so file will then be importable in any c++ module and present a PyramidalSimulation class with a run() method which will return the membrane potential at the end of execution of a fixed timestep.

4. NeuroML 2/LEMS conversion of the muscle cell model

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This version of the muscle model reflects an initial attempt to convert the model from: http://www.sciencedirect.com/science/article/pii/S0303264708001408 into NeuroML 2 (http://www.neuroml.org/neuroml2.php).

We're in the process of updating this to match the version in: https://github.com/openworm/muscle_model/tree/master/neuron_implementation

See issue: openworm/OpenWorm#169 for the latest.

See also http://www.opensourcebrain.org/projects/muscle_model/wiki.