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Readme updates #23

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Jan 3, 2015
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Readme updates #23

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39c11d2
adding Rayner to main README
slarson Jan 3, 2015
0bb9ec3
Adding link to paper, fixing text
slarson Jan 3, 2015
9e70739
adding link to image of dynamics we reproduce
slarson Jan 3, 2015
99aa44e
Adding more basic introduction
slarson Jan 3, 2015
e5082be
more intro
slarson Jan 3, 2015
1b1ee09
fixing incomplete sentence
slarson Jan 3, 2015
47d06cf
better grammar
slarson Jan 3, 2015
737243f
Adding mention of Python version
slarson Jan 3, 2015
572d9fb
Update README.md
slarson Jan 3, 2015
bcbdeb7
Reordering topics
slarson Jan 3, 2015
7f6b902
Relative links
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cf737dc
Filling in content for the first section
slarson Jan 3, 2015
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14 changes: 9 additions & 5 deletions BoyleCohen2008/README.md
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Muscle cell code from Boyle and Cohen 2008
------------------------------------------

This software was used in the publication:
This software was used in [the publication](https://groups.google.com/group/openworm-discuss/attach/df619bba6defa84f/C.%20elegans%20Body%20Wall%20Muscles%20are%20Simple%20Actuators%20-%20Boyle,%20Cohen%20-%202007.pdf?part=0.2&authuser=0):

_J.H. Boyle, N. Cohen, Caenorhabditis elegans body wall muscles are simple actuators, BioSystems 94 (2008) 170–181_

to optmise the parameters of a muscle cell model for C. elegans.
to both define and optimise the parameters of a muscle cell model for C. elegans.

**If you use or alter this code please cite the above publication.**

This will be used by the OpenWorm project to create an [initial model of a muscle cell in NeuroML 2](https://github.com/openworm/muscle_model/tree/master/NeuroML2).
This is being used by the OpenWorm project to create an [initial model of a muscle cell in NeuroML 2](https://github.com/openworm/muscle_model/tree/master/NeuroML2).

A key matlab script is located at [BoyleCohen2008/MatlabSupport/Main_Version/vclamp.m](https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/MatlabSupport/Main_Version/vclamp.m) which, when run, should produce a main graph of the paper.
A key matlab script is located at [MatlabSupport/Main_Version/vclamp.m](MatlabSupport/Main_Version/vclamp.m) which, when run, should produce a main graph of the paper.

This code is released under the terms of the MIT license.
A python version of this has been added at [PythonSupport/Main_Version/vclamp.py](PythonSupport/Main_Version/vclamp.py). When run correctly it should produce the following image:

![vclamp.py running correctly](https://cloud.githubusercontent.com/assets/1037756/5603263/93dc8866-9331-11e4-8696-cc26a85b6208.png)

This reproduces figure 2B of the Boyle & Cohen paper.

This code is released under the terms of the MIT license.
69 changes: 49 additions & 20 deletions README.md
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Expand Up @@ -5,41 +5,81 @@ Open Worm muscle model

[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/openworm/muscle_model?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

Authors: Mike Vella, Alex Dibert, Padraig Gleeson
Authors: Mike Vella, Alex Dibert, Padraig Gleeson, Rayner Lucas
email:[email protected]

If you contribute to the project please add your name to the Authors field

Introduction
------------

This repository contains several different subprojects all related to the construction of a biophysically-detailed model
of the dynamic properties of electrical excitation of the body wall muscle of the c. elegans.

![Overview of dynamics we are reproducing](https://cloud.githubusercontent.com/assets/1037756/5602898/094dd1c4-9321-11e4-9d01-bc4b73112951.png)

In the figure above, you can see the basic functionality that we are seeking to reproduce. The electrical activity of a muscle cell
can be recorded using an electrode that is stuck into it. Connecting the electrode to a sensitive
amplifier and stimulator allows a researcher to either use a [current clamp](https://en.wikipedia.org/wiki/Electrophysiology#Current_clamp) or [voltage clamp](https://en.wikipedia.org/wiki/Voltage_clamp) mode to control and examine the dynamics of the voltage changes or current flow across the membrane.

Ultimately, we understand from [Hodgkin and Huxley](https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model) that these electrical dynamics of the membrane are fully determined by the dynamics of [ion channels](https://en.wikipedia.org/wiki/Ion_channel) that sit across the membrane.

In 2008, Dr. Netta Cohen and Dr. Jordan Boyle at the University of Leeds published an article with their mathematical model of these dynamics based on real data.

This model was expressed as a system of equations and a set of parameters in their publication, as well as C++ and Matlab code.

Their original code has been graciously shared with the OpenWorm project under the BoyleCohen2008 directory. In addition, a Python port of key components of the model
has been added by OpenWorm contributors (Rayner Lucas).

For the purposes of re-using the model as a component of the larger OpenWorm project, we have converted the mathematical model of Cohen & Boyle into NeuroML2, an XML-based
description of the system of equations that make up mathematical models of biophysically-based models of excitable membranes.



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
2. NeuroML 2/LEMS conversion of the muscle cell model
3. Optimization script for the above model, utliising Optimal Neuron package. Optimizing towards sharp electrode data obtained from lab of Michael M Francis.
4. C++ Module for importation of arbitrary Pyramidal model into C++ program such as Palyanov et al SPH solver.


1. Simulation of C.Elegans muscle cell electrical properties
-----------------------------------------------------------
2. Optimization script for the above model

The authoritative version of the muscle cell model from Boyle & Cohen has been shared with the project under the [BoyleCohen2008/](BoyleCohen2008/) directory. Here you will also find a Python port of some of the scripts that demonstrate the dynamics of the muscle model.

A conversion of this model into the NEURON package is available in the [neuron_implementation/](neuron_implementation/) directory.

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

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: https://github.com/openworm/OpenWorm/issues/169 for the latest.

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


3. Optimization script for the above model
------------------------------------------

**Note: see https://github.com/openworm/muscle_model/issues/18 for details on the current status of these subprojects.**

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

3. C++ Module for SPH/muscle_model integration
4. C++ Module for SPH/muscle_model integration
----------------------------------------------

**Note: see https://github.com/openworm/muscle_model/issues/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)
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/
Expand All @@ -48,15 +88,4 @@ $ ./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
-----------------------------------------------------

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: https://github.com/openworm/OpenWorm/issues/169 for the latest.

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

[![Build Status](https://travis-ci.org/openworm/muscle_model.svg?branch=master)](https://travis-ci.org/openworm/muscle_model)