Notebook for HH model python version updated (issue #33)

openworm / hodgkin_huxley_tutorial

A repository containing code for a number of tutorials on the Hodgkin Huxley model, including an interactive Jupyter notebook

GNU Lesser General Public License v3.0

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Closed irahulsonkar closed 2 years ago

irahulsonkar commented 2 years ago

Notebook has been updated to include voltage clamp mode
Python script slightly modified for required changes in notebook
Plotting made interactive using matplotlib widget P.S. Sphinx documentation for line numbers need to be updated next.

pgleeson commented 2 years ago

Thanks @irahulsonkar, looks very good. A few small suggestions.

I notice the odes are not initialised at exactly steady state, just an approximation here: https://github.com/openworm/hodgkin_huxley_tutorial/blob/dfff6b6a87219e0f75734b535176dae5b508f919/Tutorial/Source/HodgkinHuxley.py#L215. Can you put in the values from the iclamp plots as t->∞? Should make the plots for vclamp flatter too at the start, e.g. the green plot for h above
When switching from iclamp to vclamp in the notebook, the values of simulation duration doesn't change, and stays at 140ms
Can you focus in the y axis on the part of the current input graph which is used to balance the channel current, as opposed to the very high brief pulse to change the membrane potential of the cell rapidly, i.e.

irahulsonkar commented 2 years ago

Hi @pgleeson ,

I don't think iclamp's final values (t->∞, shown below) as a initial condition to ode for vclamp will make any difference in green plot for h. X = odeint(self.dALLdt, [-64.99584, 0.05296, 0.59590, 0.31773], self.t, args=(self,)) Since, conditioning and returning voltage are set at -63.77 (as per parameter in LEMS file) the h curve will still remain same. If we change these voltages to -65 then h curve will be flat initially.
other issues are taken care of and will be pushed.

pgleeson commented 2 years ago

@irahulsonkar Thanks. Yes, I think it's fine to use the values you have here: https://github.com/irahulsonkar/hodgkin_huxley_tutorial/commit/5e15d998b6f2dab500838698767acc8cc448990f and set the conditioning/returning voltage to -65 in the standard vclamp config. There is a difference between the reversal potentials used here for na and k and the other model I was looking at from where I got the -63.77