Modelling of subcellular signalling

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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jofrony
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Joined: Thu May 10, 2018 6:37 am

Modelling of subcellular signalling

Post by jofrony »

Hi,

I am using NEURON to simulate g-protein coupled receptor signalling. I was wondering if there is a specified way in neuron to send information between point process object and distributed membrane mechanisms (for example ion channels).

I have three mechanisms which I would need to have communicating with each other:

point process -> point process -> distributed membrane mechanism

I have not found a way to connect these except by using pointers. But I would only like to have this connection at certain parts of the simulated cell.

When I insert the ion channels with pointer they will occupy a whole compartment although I would only want a segment to be modulated. To solve this, I place the whole connection on each segment but only turn on (by a modulating the single ion channel) on the specific segment I would like to modulate.

This is very elaborate way of avoiding the crash which occurs if all pointers do not have something pointing at it.

Does anyone have another solution for this?

I cannot combine the point_process because they use different solvers, one uses sparse and the other cnexp.

//jofrony
ted
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Re: Modelling of subcellular signalling

Post by ted »

When I insert the ion channels with pointer they will occupy a whole compartment although I would only want a segment to be modulated.
A segment is a compartment. Perhaps you meant to say
"When I insert the ion channels with pointer they will occupy a whole section"
but that doesn't explain everything because a pointer is only a programming construct, not a representation of an ion channel, so one cannot insert a pointer into a section or a segment.

To give you the most appropriate advice, I'll have to see the NMODL code that implements your two point processes and the density mechanism. Can you zip them up and email them to me
ted dot carnevale at yale dot edu
?
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