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Sender:王梓瑞 <wangzirui@cibr.ac.cn>

Sent At:2023 Feb. 21 (Tue.) 15:45

Recipient:NEST User Mailing List <users@nest-simulator.org>

Subject:Re: how to customize Ion channels and receptor types of "cm_default" neuron model through nestml

Hi, Charl

 

Thanks for your reply. And sorry about taking such a long time in this question. My main research interest is the biophysical model of glutamatergic cortico-striatal projections.

 

I previous constructed a striatal circuit (contain two neuron populations MSN and FSI) using simple Integrate-and-fire model, and it successfully reproduced the firing state of striatum MSN and FSI. In that case I simplified the glutamatergic cortical input from multi-synapse to single synapse.

 

Since glutamatergic cortico-striatal projections consist of AMPA and NMDA receptors, I then changed the simple Integrate-and-fire model to multi-synapse Integrate-and-fire model using NESTML. But the results didn't seem good, and got even worse when I handly tuned some parameters. I have been confused for a long time and I thought my multi-synapse definition might account for this.

 

 I read about "cm_default" neuron model on NEST model directory, which you described containing AMPA_NMDA receptors. And the difference between your definition on this receptor and mine is the term of NMDA ratio (ratio of NMDA versus AMPA channels). So I thought that might help me resolve this issue and that's why I wrote to ask how to customize receptor types of "cm_default" neuron model through NESTML.

 

So briefly:

I wonder how I can apply the NMDA ratio in my own multi-synapse Integrate-and-fire model or is it possible to extract the AMPA_NMDA receptors from "cm_default".

 

And I read about the "cm_default" neuron model on NEST model directory, and you described like "For receptors, the choice is AMPA, GABA or NMDA or AMPA_NMDA. Ion channels and receptor types can be customized with NESTML."

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Sender:Charl Linssen <nest-users@turingbirds.com>

Sent At:2022 Dec. 8 (Thu.) 16:56

Recipient:users <users@nest-simulator.org>

Subject:[NEST Users] Re: how to customize Ion channels and receptor types of "cm_default" neuron model through nestml

Dear Zirui,

Thank you for writing in. Just to double-check, the compartmental ("cm_default") model in NEST is intended for use in morphologically detailed models, containing dozens or hundreds of compartments. If your model can be described by only a few compartments, it could be easier to manually define these (define say a separate membrane potential and dendritic potential and the coupling between them; see https://nestml.readthedocs.io/en/v5.1.0/tutorials/active_dendrite/nestml_active_dendrite_tutorial.html for an example).

If you do indeed need the full morpological complexity in your simulations, then the cm_default model is indeed the way to go. We are currently working on extending NESTML to support defining the biophysics in NESTML (ion channels, membrane dynamics etc.) and then combining this with a morphology in NEST. For a prototype of this functionality, please see the branch in https://github.com/nest/nestml/pull/772. The current effort there is focused on adding the ability to specify different ion channels in a more flexible manner.

If you could describe a little bit more about your use case and what exactly you are trying to achieve, we could probably give you some more specific advice.

Cheers,

Charl

On Mon, Dec 5, 2022, at 05:54, 王梓瑞 wrote:

Dear nest community,

I wonder if any of you know how to customize Ion channels and receptor types of "cm_default" neuron model through nestml.

I noticed some information on Extending NESTML- Running NESTML with custom templates, but I still found myself confused due to my poor understanding.

Is there any way to acquire the .nestml file of the cm_default neuron model?

Thank you.

Best,

Zirui

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