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openworm / CElegansNeuroML

NeuroML based C elegans model, contained in a neuroConstruct project, as well as c302
http://opensourcebrain.org/projects/celegans
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Attempt to match named cells in Kato paper #61

Closed slarson closed 8 years ago

slarson commented 8 years ago

Match time run in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034

@pgleeson -- running into a problem. I tried to get the NEURON plot working so I added an argument to runAndPlot.py. Works perfectly except it is plotting all 302 neurons instead of only the several dozen that I indicated in the LEMS file. How do I get the NEURON output to respect the cells_to_plot list?

slarson commented 8 years ago

Second problem -- when trying to simulate and render 64800 milliseconds, NEURON is OK but during plotting, I'm getting "Killed": https://gist.github.com/slarson/ded5cf9da1a5b914d6cc8f62180ea0b5 Ever seen this before @pgleeson ?

pgleeson commented 8 years ago

Probably an issue with running a long sim and then reloading all of the data incl for 96 muscles. Look at the size of the data files produced.

You could just generate the simulation using c302, run it manually, save the data and make a python script to just reload the subset of cells you want to plot.

slarson commented 8 years ago

I'll try that-- thanks