Define parameters for simulated experiment using jNeuroML on the command line, based on the methods that went into the figure

[slarson]

Here's the figure:

Key points to test:

• Run the muscle model in voltage clamp mode
• modulate voltage for ~1s in a square pulse as shown.
• should result in initial current amplitude change of ~160 pA
• should decay to steady state of ~70 pA until voltage is released
• time constants of decay should match both figures
• Do the equivalent test for the impulse in the second figure on the right

It is not clear exactly what voltage to modulate to -- therefore use trial and error initially to pick a value that will result in the correct initial current amplitude and test if the other parameters are consistent. Otherwise, work out the correct voltage amount via information in the paper.

direct link to paper

This unit test should be instrumented to run in Travis-CI

FYI @rayner @VahidGh @rgerkin @ahrasheed

[rgerkin]

@slarson @pgleeson
Is there an existing procedure for regenerating the LEMS file (LEMS_NeuronMuscle.xml) with the desired parameters, other than simply editing the file, by analogy to NMLChannelAnalyse for the channel files?

[slarson]

@rgerkin I think what you are describing is what we want to do with #18 -- running the cell-level LEMS file through an optimization process to pick desired parameters.

[travs]

This would be complete if we had the exact shell command(s) that runs the muscle model under the right set of parameters.

[pgleeson]

Looking at Figure 1 more closely, isn't this more relevant to the properties of the current elicited by shining light on the channelrhodopsin expressing muscle cell? Aren't they trying to see what current that stimulation produces, rather than find the intrinsic properties of the muscle channels?

We couldn't really reproduce this in LEMS unless there was channel which would simulate the photocurrent and then it wouldn't help with tuning the rest of the cell properties...

[slarson]

I'm pretty sure the effect of activating the light sensitive channels can be modeled as a current injection.

[VahidGh]

Actually, this could be a beautiful example of proofing how traditional Hodgkin-Huxley approach fails to model such a curve for single-channel modeling!
As could be inferred from this figure, Channelrhodopsin-2 has 4 different states, that can not be modeled using 2 same exponentially-controlled states, as usually being considered in HH models.
If we can not model such a kinetic using HH models, then we should reconsider the assumption of only using HH models, at least for channel modeling, and also consider Markov models if such channels exists in C. elegans.
And if we can finally model this, as Stephen mentioned, the final result would be useful for validating existing model proposed by Boyle&Cohen.

[rgerkin]

At the timescales we are interested in, is there any evidence that the ChR2 state transitions are important for predicting the membrane potential time course? I don't want to ignore channel details when it comes to real channels, but ChR2 is a tool, not a natural part of the organism, so if modeling its response to pulses of light as a current (or conductance) injection is sufficient, then I think there's no need to go any further.