Generating current/voltage relationship files

[travs]

The ability to make a LEMS simulation that generates I/V relationships at each voltage was given by these lines in the template from Channelpedia.

The generated i_*.lems.dat files were used by Rayner's script to produce an I/V plot, which is useful for ChannelWorm's goal of comparing simulated and real ion channel data.

PyNeuroML seems to have most of the functionality we need at this point, except that the built in template doesn't produce these files.

I'm wondering if we should implement this in the template used in PyNeuroML's channel analysis, or if there was a reason the functionality was removed (too many dat files perhaps?)

[pgleeson]

Yes, that was removed due to the large number of i_*.lems.dat files produced.

I've reenabled it, but made generating these files optional, using the -ivCurve option, e.g. this:

pynml-channelanalysis -temperature 34   -minV -55  -maxV 80  -duration 600  \
         -clampBaseVoltage -55  -clampDuration 580  -stepTargetVoltage 10  \ 
          -erev 50  -caConc 0.001 -clampDuration 600 -stepTargetVoltage 5 \
          -ivCurve ca_boyle.channel.nml 

will generate (and save as ca_boyle.i_peak.dat) the holding voltages vs current for ca_boyle.channel.nml:

Might be what you and @VahidGh need for generating the iv curves.

Not all parameters above are required, but the erev parameter is very important to produce a correct IV curve...

[VahidGh]

@pgleeson, that's great, thanks.

[travs]

Okay this is awesome! Thanks @pgleeson

[travs]

Having some trouble running this with another ion channel (not ca_boyle) as input.

Edit: Got it to work. The plots weren't showing up because my terminal was fullscreen.....

[pgleeson]

Great. Btw, you had 2 -clampDurations there and also erev of 50mV for k chan is probably wrong. Also no need for caConc...

[travs]

Ok, I just copied it from the example to see if could get some output. So ca_boyle can be run with two clamp durations? Are there two separate simulations or something?

[pgleeson]

My mistake. Sorry...

[travs]

Ok, no sweat; we can chat about this in our meeting tomorrow!

[rgerkin]

@travs @pgleeson When are you meeting?

[rgerkin]

My pull request here will do the same thing using the same code, but allow you to do it from within a python script, rather than from a shell. You would use pyneuroml.analysis.NML2ChannelAnalysis.run(), with keyword arguments matching the ones @pgleeson's first comment above.

[pgleeson]

Btw @rgerkin, it was just an informal meeting during the HBP meeting last week that @slarson and I were at and had a quick hangout with @travs