Closed christian-oreilly closed 1 year ago
I just had a look at the schema docs, and various bits of the gates are exposed (the "dynamics" tab):
https://docs.neuroml.org/Userdocs/Schemas/Channels.html#gatehhrates
Are you looking for q
?
There are also utilities to analyse channels:
https://docs.neuroml.org/Userdocs/VisualisingChannels.html
The list_recording_paths_for_exposures
method only provides an incomplete list that can be obtained from the model description. (The complete list of exposures requires the model to be instantiated)
These figures
show the dynamics (tau) and steady state for a given gating process (e.g., h: inactivation, m: activation). However, they do not allow us to see how h and m vary with time during the simulation. For that, it would require and exposure
similar to iChannel
. I am not sure what q
stands for, but I supposed it was related to temperature (as in q10
)...?
Ah, yeh, q
is not related to q10
. q
is what we're looking for here. The gate itself will have id h
or m
, but the variable in the component that is exposed as the value of the activation variable is q
. Here is an example of recording/plotting rate variables:
Yes, q is what you require, e.g. for the HH model at https://github.com/NeuroML/NeuroML2/blob/master/LEMSexamples/LEMS_NML2_Ex5_DetCell.xml, m, h, n can be plotted with:
<Display id="d2" title="Ex5: HH cell with simple morphology: rate variables" timeScale="1ms" xmin="0" xmax="300" ymin="-0.1" ymax="1.1">
<Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1" color="#000000" timeScale="1ms"/>
<Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1" color="#ff0000" timeScale="1ms"/>
<Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1" color="#0000ff" timeScale="1ms"/>
</Display>
Note: the gate has id m, etc and the variable inside there with its value is called q, e.g. see https://github.com/NeuroML/NeuroML2/blob/master/NeuroML2CoreTypes/Channels.xml#L246-L263
I looked at the documentation on
exposures
and tried to find the different paths available usinglist_recording_paths_for_exposures
but I could not find a way to get the times-series describing the activation and inactivation variables of HH models. I can get the overall current for a given type of ion currents usingiDensity
, e.g., in my casebut I could not find a way to get the activation and inactivation alone. Is it something possible? If not, I think that could be a useful feature as it is convenient to see these gating states to better understand the dynamics of models.