I'm trying to use my own short term potentiation model with an existing model. The model is the IF_cond_exp model from PyNN. I tried your nestml integrate and fire models from Git.../nestml/master/models/neurons, and none seem to be the IF_cond_exp model. The closest I could find was the iaf_cond_beta_neuron. Am I missing something. Is the IF_cond_exp model done somewhere in nestml? (I'm relatively vested in that IF_cond_exp model. I need the nestml neuron model before I can properly use the nestml synapse model.) -Chris

From: Charl Linssen nest-users@turingbirds.com Sent: 23 July 2024 11:25 To: users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

You don't often get email from nest-users@turingbirds.commailto:nest-users@turingbirds.com. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification Hi Chris,

Thank you for writing in! It would be great to have a better compatibility and better documentation for using NESTML models in pyNN, but as of now this is not yet in place, please let us know if you have any tips or experience to share.

On SpiNNaker, only neuron models are supported for now, we have an open position for a student project to implement synaptic plasticity as well!

With kind regards, Charl

On Mon, Jul 22, 2024, at 16:32, Chris Huyck wrote:

I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN).

-Chris _______________________________________________ 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

I finally got to this. It looks like it has the same parameters (though different names). Some paramters (for example C_m cm) have different values, so it's a funny search to find the identical models. I'll persevere. -Chris

From: Charl Linssen nest-users@turingbirds.com Sent: 10 February 2025 11:00 To: users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

Hey Chris,

Sorry, due to a glitch in the mailing list I only saw this message now.

Is https://github.com/nest/nestml/blob/master/models/neurons/iaf_cond_exp_neuro... the model that you are looking for?

Cheers, Charl

On Fri, Jan 31, 2025, at 13:10, Chris Huyck wrote:

I'm trying to use my own short term potentiation model with an existing model. The model is the IF_cond_exp model from PyNN. I tried your nestml integrate and fire models from

Git.../nestml/master/models/neurons, and none seem to be the IF_cond_exp model. The closest I could find was the iaf_cond_beta_neuron. Am I missing something. Is the IF_cond_exp model done somewhere in nestml? (I'm relatively vested in that IF_cond_exp model. I need the nestml neuron model before I can properly use the nestml synapse model.)

-Chris

From: Charl Linssen <nest-users@turingbirds.commailto:nest-users@turingbirds.com> Sent: 23 July 2024 11:25 To: users@nest-simulator.orgmailto:users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

You don't often get email from nest-users@turingbirds.commailto:nest-users@turingbirds.com. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Hi Chris,

Thank you for writing in! It would be great to have a better compatibility and better documentation for using NESTML models in pyNN, but as of now this is not yet in place, please let us know if you have any tips or experience to share.

On SpiNNaker, only neuron models are supported for now, we have an open position for a student project to implement synaptic plasticity as well!

With kind regards,

Charl

On Mon, Jul 22, 2024, at 16:32, Chris Huyck wrote:

I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN).

-Chris

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Yes, I think I've seen it before. I tried the iaf_cond_exp_neuron you suggested, and it doesn't really work the same, as the standard model from pyNN. I got pretty close with iaf_psc_exp_neuron. One issue is that several of the parameter values (particular C_m) are doing something quite different in the standard model (default 1.0) and the iaf_cond_exp model (default 250.0). Another, which is really odd, is some extra parameters seem to appear that aren't in the nestml code beta_Ca and tau_Ca just appear in both of the pyNN parameter lists from the nestml code. There are also some issues with the startup voltage, but I just let it run for a while so it goes to the rest level.

I'm considering digging through the nest code to see what is actually implemented, and then do that in nestml. If I do that, I'll mail it to you.

As for findability, it would be nice to have a root to the models. The problem, I find, is that there are lots of roots and versions. Nest, pyNN and now nestML have different systems. These of course are also complicated by different versions. That nestml link you just sent could reasonably connect to the git page, though versioning is difficult.

Thanks for your help, -Chris

From: Charl Linssen nest-users@turingbirds.com Sent: 13 February 2025 15:00 To: users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

Hi Chris,

Have you seen the models index on https://nestml.readthedocs.io/en/latest/models_library/index.html?

If you have any tips on ways in which we could improve model findability, then please let me know!

Cheers, kind regards, Charl

On Thu, Feb 13, 2025, at 15:02, Chris Huyck wrote:

I finally got to this. It looks like it has the same parameters (though different names). Some paramters (for example C_m cm) have different values, so it's a funny search to find the identical models. I'll persevere.

-Chris

From: Charl Linssen <nest-users@turingbirds.commailto:nest-users@turingbirds.com> Sent: 10 February 2025 11:00 To: users@nest-simulator.orgmailto:users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

Hey Chris,

Sorry, due to a glitch in the mailing list I only saw this message now.

Is https://github.com/nest/nestml/blob/master/models/neurons/iaf_cond_exp_neuro... the model that you are looking for?

Cheers,

Charl

On Fri, Jan 31, 2025, at 13:10, Chris Huyck wrote:

I'm trying to use my own short term potentiation model with an existing model. The model is the IF_cond_exp model from PyNN. I tried your nestml integrate and fire models from

Git.../nestml/master/models/neurons, and none seem to be the IF_cond_exp model. The closest I could find was the iaf_cond_beta_neuron. Am I missing something. Is the IF_cond_exp model done somewhere in nestml? (I'm relatively vested in that IF_cond_exp model. I need the nestml neuron model before I can properly use the nestml synapse model.)

-Chris

From: Charl Linssen <nest-users@turingbirds.commailto:nest-users@turingbirds.com> Sent: 23 July 2024 11:25 To: users@nest-simulator.orgmailto:users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

You don't often get email from nest-users@turingbirds.commailto:nest-users@turingbirds.com. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Hi Chris,

Thank you for writing in! It would be great to have a better compatibility and better documentation for using NESTML models in pyNN, but as of now this is not yet in place, please let us know if you have any tips or experience to share.

On SpiNNaker, only neuron models are supported for now, we have an open position for a student project to implement synaptic plasticity as well!

With kind regards,

Charl

On Mon, Jul 22, 2024, at 16:32, Chris Huyck wrote:

I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN).

-Chris

_______________________________________________

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

_______________________________________________

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

_______________________________________________ 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

My stp model is pretty dodgy at the moment. It's Hebbian but it's entirely linear in both growth and decay. I'm going to look around the literature a bit and see if I can have it a bit more biologically motivated. If you want it now, I can send it. -Chris

From: Charl Linssen nest-users@turingbirds.com Sent: 14 February 2025 11:37 To: users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

Hi Chris,

Thanks for the detailed feedback! Indeed, there can be quite a big "model zoo" of different variants, even for a model that is ostensibly the same. As you noticed, this can be the case for normalised parameter values (like having a C_m of 1, or a resting potential of 0 rather than -70 mV), but it could apply to details of the dynamical equations (ODEs) as well.

When a model is used in the context of NEST, its C++ class derives from other classes that implement other functionality, for instance, structural plasticity. These superclasses have their own parameters, like beta_Ca and tau_Ca for the structural plasticity feature.

If there is a new model variant that you need to implement, please consider contributing it as a pull request to the NESTML repository afterwards! We are also working on an "include" statement in NESTML that will make it much cleaner and more modular to have different variants of a model.

Thanks again and please don't hesitate to get in touch if anything is unclear or not working right.

Yours, Charl

On Thu, Feb 13, 2025, at 17:47, Chris Huyck wrote:

Yes, I think I've seen it before. I tried the iaf_cond_exp_neuron you suggested, and it doesn't really work the same, as the standard model from pyNN. I got pretty close with iaf_psc_exp_neuron. One issue is that several of the parameter values (particular C_m) are doing something quite different in the standard model (default 1.0) and the iaf_cond_exp model (default 250.0). Another, which is really odd, is some extra parameters seem to appear that aren't in the nestml code beta_Ca and tau_Ca just appear in both of the pyNN parameter lists from the nestml code. There are also some issues with the startup voltage, but I just let it run for a while so it goes to the rest level.

I'm considering digging through the nest code to see what is actually implemented, and then do that in nestml. If I do that, I'll mail it to you.

As for findability, it would be nice to have a root to the models. The problem, I find, is that there are lots of roots and versions. Nest, pyNN and now nestML have different systems. These of course are also complicated by different versions. That nestml link you just sent could reasonably connect to the git page, though versioning is difficult.

Thanks for your help,

-Chris

From: Charl Linssen <nest-users@turingbirds.commailto:nest-users@turingbirds.com> Sent: 13 February 2025 15:00 To: users@nest-simulator.orgmailto:users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

Hi Chris,

Have you seen the models index on https://nestml.readthedocs.io/en/latest/models_library/index.html?

If you have any tips on ways in which we could improve model findability, then please let me know!

Cheers, kind regards,

Charl

On Thu, Feb 13, 2025, at 15:02, Chris Huyck wrote:

I finally got to this. It looks like it has the same parameters (though different names). Some paramters (for example C_m cm) have different values, so it's a funny search to find the identical models. I'll persevere.

-Chris

From: Charl Linssen <nest-users@turingbirds.commailto:nest-users@turingbirds.com> Sent: 10 February 2025 11:00 To: users@nest-simulator.orgmailto:users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

Hey Chris,

Sorry, due to a glitch in the mailing list I only saw this message now.

Is https://github.com/nest/nestml/blob/master/models/neurons/iaf_cond_exp_neuro... the model that you are looking for?

Cheers,

Charl

On Fri, Jan 31, 2025, at 13:10, Chris Huyck wrote:

I'm trying to use my own short term potentiation model with an existing model. The model is the IF_cond_exp model from PyNN. I tried your nestml integrate and fire models from

Git.../nestml/master/models/neurons, and none seem to be the IF_cond_exp model. The closest I could find was the iaf_cond_beta_neuron. Am I missing something. Is the IF_cond_exp model done somewhere in nestml? (I'm relatively vested in that IF_cond_exp model. I need the nestml neuron model before I can properly use the nestml synapse model.)

-Chris

From: Charl Linssen <nest-users@turingbirds.commailto:nest-users@turingbirds.com> Sent: 23 July 2024 11:25 To: users@nest-simulator.orgmailto:users@nest-simulator.org Subject: [NEST Users] Re: nestml synapses in pyNN

You don't often get email from nest-users@turingbirds.commailto:nest-users@turingbirds.com. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Hi Chris,

Thank you for writing in! It would be great to have a better compatibility and better documentation for using NESTML models in pyNN, but as of now this is not yet in place, please let us know if you have any tips or experience to share.

On SpiNNaker, only neuron models are supported for now, we have an open position for a student project to implement synaptic plasticity as well!

With kind regards,

Charl

On Mon, Jul 22, 2024, at 16:32, Chris Huyck wrote:

I've taken your noisy_synapse model and got that to run in pyNest. When I try it in PyNN it fails (can't find weight if you set w, weight not an argument if you use weight). I understand that you don't support pyNN. Do you support SpiNNaker (as it's a target)? If so, how do you access the model on SpiNNaker? (I only access SpiNNaker through PyNN).

-Chris

_______________________________________________

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

_______________________________________________

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

_______________________________________________

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

_______________________________________________ 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