Apply the analysis code for Kato-like visualizations to c302

[slarson]

This issue captures the effort to be able to visualize c302 output in a PCA'd plot, as shown in the readme of this repo. This has already been done with real data, now the effort is to be able to have somewhat comparable pictures that come out of the simulation.

Originally this was captured by issues openworm/OpenWorm#114 and openworm/OpenWorm#115. Moving this over here for now.

[slarson]

By the way, it looks like we did have a contributor @Alexander-N who had a first attempt at something like this here:

https://github.com/openworm/NEURONSimData/pull/1/files

Alexander -- sorry it has taken so long to get back to this!!

[slarson]

A bit of explanation. The repo here: https://github.com/openworm/NEURONSimData was an early attempt to pull data out that required downloading and running NEURON and using it correctly. This was a tough thing for many contributors to do, and despite our attempts to make tutorials to help, most folks were not able to use it very effectively.

When c302 came along, this made things easier, and the only thing that really needed to be resolved was everybody being able to install it OK. Consequently the repo contents of https://github.com/openworm/NEURONSimData are now a bit out dated, because the output from NEURON looks different than the output from c302.

[lukeczapla]

@slarson we've been making a lot of progress in analysis, @theideasmith has done a lot of work. I have a question (related to above description of how sims are executed), are the c302 simulations done in the jNeuroML code? I'm trying to grab that repo because I managed to just put the LEMS XML and NML files and related XML data into it's own folder and just run jnml to execute the simulation (and I see java is using 300% CPU resources while this runs). One of the outputs coming out is calcium concentration for all the 302 cells.