Update README.md with new sections

[slarson]

• [x] Better introduction to the repository as a whole, its purpose, what it is trying to accomplish
• [ ] Instructions on how to run the vclamp.py and explain its significance to the Boyle/ Cohen paper
• [ ] Instructions on how to run the latest example ion channel models
  • [ ] Explanation of what each of the plots actually mean that are generated
  • [ ] Explanation of how to derive an I/ V plot and why that's important (ivanalyze.py)
• [ ] Pointer to the journal club material explaining hodgkin huxley dynamics
• [ ] Pointer to the tests that are being automatically run on ion channels
• [ ] Explanation of the context of the synapse and motor neuron and how this is establishing a set of tools to continue modeling on up from here.
• [ ] How to run the Figure.xmls

[rayner]

The iv_analyse.py script (and, I think, the LEMS template that dumps the current values to a file) only exists on my fork of the BlueBrainProjectShowcase repo at the moment. I'm not entirely sure where to put them, as they're entirely dependent on the BlueBrainProjectShowcase code but are really part of the muscle model work.

[slarson]

@rayner What if we include the BlueBrainProjectShowcase code as a dependency to make it run within this repo?

[pgleeson]

It would be best to update the individual readmes in the sub directories with the specific details of that code and keep the top level Readme quite brief.

Also, it would be best to check again and see if the first 2 items in the main readme are still valid. @vellamike changed pyramidal quite a lot since first making these and if the code can't be run with the instructions that are there, the details should be moved to a readme in the relevant folders and a pointer put in the main readme to them mentioning that it's legacy code. libNeuroML has moved on quite a bit since then and a script in Python/libNeuroML generating Neuron code (as in c302) covers most of the use case of a pyramidal based script. @vellamike would you agree? We can close this issue then.

[pgleeson]

Re the iv_analyse.py script, the latest merge includes the BlueBrainProjectShowcase code to test the analyse_ca_boyle.sh scripts. However generating iv plots etc. is more of an exploration of the behaviour of the code rather than a test, so it's probably not too much of an issue if they're not included in the main tests yet.

More important would be making sure the NeuroML2 model is identical to the Matlab/python version, as it's much easier to reproduce the iv plots of the paper from the Matlab etc & get some insight from them. I've suggested a Python script that would be useful for this here: https://github.com/openworm/muscle_model/issues/13#issuecomment-65214680

[pgleeson]

As mentioned above, the READMEs are still causing confusion, so i've updated the main one pointing to this issue https://github.com/openworm/muscle_model/issues/18.

[slarson]

[slarson]

Parking this one too.