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Muscle Model Explorer Public

OpenWorm

Understand the way the muscle model is built up via NeuroML2 to produce cell membrane dynamics!

Required Evidence

Earn the pre requisite badges

Screenshot of your badgelist profile with the Hodgkin-Huxley tutorial badge (http://bit.ly/2bJO9VW) and the Muscle Model builder badge (http://bit.ly/2bKjCTw) successfully earned. More Info

Run explorer code

Successfully run the code in the muscle model explorer iPython notebook (http://bit.ly/2c6GO2c). Run in the NeuroML2 directory! Notebook environment not required. Copy the input and output as text, paste at http://gist.github.com and link here. More Info

Run the figure 2A code & compare to paper

On the command line in the NeuroML2 directory, run: pynml LEMS_Figure2A.xml Find figure 2A in the Boyle & Cohen 2008 paper. (http://bit.ly/2cjXnce) Take a single screenshot with paper and model figures. Arrange the model figure that most closely matches the paper figure next to each other. More Info

Run the figure 2B code & compare to paper

On the command line in the NeuroML2 directory, run: pynml LEMS_Figure2B.xml Find figure 2B in the Boyle & Cohen 2008 paper. (http://bit.ly/2cjXnce) Take a single screenshot with paper and model figures. Arrange the model figure that most closely matches the paper figure next to each other. More Info

Explain the figures

In your own words, explain what the 2A & 2B figures are showing, beyond just the figure titles. Do you see a connection between the last block of the notebook and some of the figures? If so, use your own words to explain. More Info

Badge Overview

The muscle model project in the OpenWorm project (http://github.com/openworm/muscle_model) is open source code that contains multiple implementations of a published model of c. elegans muscle membrane dynamics.  

Earning this badge will show you how to compare and interpret the output of the muscle model with figures in published papers.

Badge Experts

 

Marc Miranda

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Badge awarded on 9/22/16
 

Mauricio Fonseca

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Badge awarded on 8/17/17
 

Neil Shah

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Badge awarded on 9/22/16
 

Ramin M. Hasani

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Badge awarded on 10/8/16
 

Shubham Singh

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Badge awarded on 8/17/17

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Claus Agerskov

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