Re: how to customize Ion channels and receptor types of "cm_default" neuron model through nestml
21 Feb
2023
21 Feb
'23
8:45 a.m.
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."
------------------------------------------------------------------
Sender:Charl Linssen <nest-users(a)turingbirds.com>
Sent At:2022 Dec. 8 (Thu.) 16:56
Recipient:users <users(a)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_ac…
<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
<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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org <mailto:users@nest-simulator.org
>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org >
9 Mar
9 Mar
3:32 a.m.
New subject: how to customize Ion channels and receptor types of "cm_default" neuron model through nestml
Hi,
Can I have the NESTML file of the "cm_default" neuron model to refer to if
it's not a problem for you?
Thanks a lot in advance!
Best,
Zirui
------------------------------------------------------------------
Sender:王梓瑞 <wangzirui(a)cibr.ac.cn>
Sent At:2023 Feb. 21 (Tue.) 15:45
Recipient:NEST User Mailing List <users(a)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."
------------------------------------------------------------------
Sender:Charl Linssen <nest-users(a)turingbirds.com>
Sent At:2022 Dec. 8 (Thu.) 16:56
Recipient:users <users(a)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_ac…
<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
<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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org <mailto:users@nest-simulator.org
>
To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave@nest-simulator.org >
3:53 p.m.
New subject: how to customize Ion channels and receptor types of "cm_default" neuron model through nestml
Dear Zirui,
The cm_default model in NEST was written by hand and not generated from NESTML code. As
you are not working with a morphologically detailed compartmental neuron, it might make
more sense to not use the compartmental models feature, but instead to write out the
dynamics of your individual ion channels by hand in the NESTML file. See for example here:
https://github.com/nest/nestml/blob/master/models/neurons/wb_cond_multisyn.…
Please let us know if that approach would work for you.
With kind regards,
Charl
On Thu, Mar 9, 2023, at 03:32, 王梓瑞 wrote:
Hi,
Can I have the NESTML file of the "cm_default" neuron model to refer to if
it's not a problem for you?
Thanks a lot in advance!
Best,
Zirui
------------------------------------------------------------------
Sender:王梓瑞 <wangzirui(a)cibr.ac.cn>
Sent At:2023 Feb. 21 (Tue.) 15:45
Recipient:NEST User Mailing List <users(a)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."
------------------------------------------------------------------
Sender:Charl Linssen <nest-users(a)turingbirds.com>
Sent At:2022 Dec. 8 (Thu.) 16:56
Recipient:users <users(a)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_ac…
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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
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Charl Linssen -
王梓瑞