Hi all - I'm aiming to run simulations using Izhikevich's neuron model (or another efficient model with spike generation), two dendritic compartments, two glutamate receptor subtypes, and temporal synaptic dynamics. My understanding is that Nest supports the Izhikevich neuron model with instantaneous current injection (i.e. no synaptic dynamics), the iaf_cond_alpha_mc neuron model for multiple compartments, the aeif_cond_alpha_multisynapse model for multiple receptor subtypes, and any of the _psc_ or _cond_ neuron models for synaptic dynamics. Am I looking at multiple choice here? I.e. I can't use a single neuron model with all of these features? If so, does anyone know of any Nest add-ons that efficiently handle all the features above? I'd be grateful for any advice.
Best
Dominic
Dear Dominic,
as you have correctly found out yourself, neuron models in NEST come - in contrast to other simulators - in one piece. Each of them is implemented as an individual C++ class and there is no compositionality of features on that level.
As I see it, you have two possibilities:
* Write your own neuron model in C++ that has all the features you want. As a starting point for this, it would probably be easiest to start with the code of the existing model that is closest to what you want and add the other features by copying them from the models you already found having them.
* Use the NEST Modeling Language NESTMLhttps://github.com/nest/nestml to write your model. This offers a much higher level of abstraction and NESTML’s toolchain will then generate the C++ code for you.
I suggest you use the second approach, as that frees you from dealing with all the details of the model API of NEST. Feel free to ask more detailed questions here in case you don’t get along with the documentation and tutorial material for NESTML.
Cheers, Jochen!
On 02.12.20 21:48, d.standage@bham.ac.ukmailto:d.standage@bham.ac.uk wrote:
Hi all - I'm aiming to run simulations using Izhikevich's neuron model (or another efficient model with spike generation), two dendritic compartments, two glutamate receptor subtypes, and temporal synaptic dynamics. My understanding is that Nest supports the Izhikevich neuron model with instantaneous current injection (i.e. no synaptic dynamics), the iaf_cond_alpha_mc neuron model for multiple compartments, the aeif_cond_alpha_multisynapse model for multiple receptor subtypes, and any of the _psc_ or _cond_ neuron models for synaptic dynamics. Am I looking at multiple choice here? I.e. I can't use a single neuron model with all of these features? If so, does anyone know of any Nest add-ons that efficiently handle all the features above? I'd be grateful for any advice.
Best
Dominic _______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Thanks, Jochen - that helps!
Dominic
Dominic Standage, PhD Marie Curie Senior Research Fellow School of Psychology / Centre for Computational Neuroscience and Cognitive Robotics University of Birmingham Birmingham, B15 2TT United Kingdom Email - d.standage@bham.ac.uk Web - www.standage.nethttp://www.standage.net ________________________________ From: j.eppler@fz-juelich.de j.eppler@fz-juelich.de Sent: 02 December 2020 16:06:31 To: NEST User Mailing List; Dominic Standage (Psychology) Subject: Re: [NEST Users] Combining neuron model features
Dear Dominic,
as you have correctly found out yourself, neuron models in NEST come - in contrast to other simulators - in one piece. Each of them is implemented as an individual C++ class and there is no compositionality of features on that level.
As I see it, you have two possibilities:
* Write your own neuron model in C++ that has all the features you want. As a starting point for this, it would probably be easiest to start with the code of the existing model that is closest to what you want and add the other features by copying them from the models you already found having them.
* Use the NEST Modeling Language NESTMLhttps://github.com/nest/nestml to write your model. This offers a much higher level of abstraction and NESTML’s toolchain will then generate the C++ code for you.
I suggest you use the second approach, as that frees you from dealing with all the details of the model API of NEST. Feel free to ask more detailed questions here in case you don’t get along with the documentation and tutorial material for NESTML.
Cheers, Jochen!
On 02.12.20 21:48, d.standage@bham.ac.ukmailto:d.standage@bham.ac.uk wrote:
Hi all - I'm aiming to run simulations using Izhikevich's neuron model (or another efficient model with spike generation), two dendritic compartments, two glutamate receptor subtypes, and temporal synaptic dynamics. My understanding is that Nest supports the Izhikevich neuron model with instantaneous current injection (i.e. no synaptic dynamics), the iaf_cond_alpha_mc neuron model for multiple compartments, the aeif_cond_alpha_multisynapse model for multiple receptor subtypes, and any of the _psc_ or _cond_ neuron models for synaptic dynamics. Am I looking at multiple choice here? I.e. I can't use a single neuron model with all of these features? If so, does anyone know of any Nest add-ons that efficiently handle all the features above? I'd be grateful for any advice.
Best
Dominic _______________________________________________ NEST Users mailing list -- users@nest-simulator.orgmailto:users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.orgmailto:users-leave@nest-simulator.org
-- Dr. Jochen Martin Eppler Phone: +49(2461)61-96653 ---------------------------------- Simulation Laboratory Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation
------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
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d.standage＠bham.ac.uk -
Dominic Standage
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Jochen Martin Eppler