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aeif_cond_beta_multisynapse in NESTML

MPI-based error on v3.8

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tanguy.damart＠protonmail.com

8 Oct 2024 8 Oct '24

10:44 a.m.

Hello everyone, Is there a NESTML version of the NEST model aeif_cond_beta_multisynapse ? (https://nest-simulator.readthedocs.io/en/stable/models/aeif_cond_beta_multi…) If not, is there any difficulties that I might face implementing it in NESTML that I need to be aware of ? (Like how to handle multiple types of synapses). Best, Tanguy

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Charl Linssen

8 Oct 8 Oct

1:55 p.m.

Hi Tanguy, Thanks for writing in! It shouldn't be any problem to implement this neuron using NESTML. You could take several existing models, and add together the elements into a new file. (We'd also love to have the model in our repository, if you would like to make a pull request with the model and some unit test afterwards, that would be great!) For the base aeif model: https://github.com/nest/nestml/blob/master/models/neurons/aeif_cond_alpha_n… For the beta kernel: https://github.com/nest/nestml/blob/master/models/neurons/iaf_cond_beta_neu… For multiple input ports: https://github.com/nest/nestml/blob/master/models/neurons/traub_cond_multis… Please note that we are in the process of reviewing/merging a pull request related to refractoriness which could be of relevance to your development, please see https://github.com/nest/nestml/pull/1100 for the new preferred way of implementing absolute refractoriness. We are also working on an "include" statement, that will allow you to include one file (for instance, containing the beta kernel) from another file (the neuron model), making NESTML much more modular. Stay tuned, and please let us know how you fare! With kind regards, Charl On Tue, Oct 8, 2024, at 10:44, tanguy.damart(a)protonmail.com wrote:

Hello everyone, Is there a NESTML version of the NEST model aeif_cond_beta_multisynapse ? (https://nest-simulator.readthedocs.io/en/stable/models/aeif_cond_beta_multi…) If not, is there any difficulties that I might face implementing it in NESTML that I need to be aware of ? (Like how to handle multiple types of synapses). Best, Tanguy _______________________________________________ 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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Tanguy Damart

11 Oct 11 Oct

10:33 a.m.

Hi Charl, Thank you for the pointers, I made good progress on the model using the traub_cond_multisyn_neuron.nestml since it has the four synpatic types I was interested in. However, I am still having some troubles with the input ports. I implemented my ports as in the traub model as: """ input: AMPA <- spike NMDA <- spike GABA_A <- spike GABA_B <- spike I_stim pA <- continuous """ But I read in the doc "an unmarked port will by default handle all incoming presynaptic spikes." Does that mean that when creating the connections, I cannot connect to one specific synapse type ? I tried: """ nest.Connect(noise, neuron, syn_spec={"synapse_model": "AMPA"}) """ and """ nest.Connect(noise, neuron, syn_spec={"synapse_model": "static_synapse", "receptor_type": "AMPA"}) """ and both failed. Could you let me know how to proceed ? Cheers, Tanguy On Tuesday, 8 October 2024 at 19:55, Charl Linssen <nest-users(a)turingbirds.com> wrote:

Hi Tanguy, Thanks for writing in! It shouldn't be any problem to implement this neuron using NESTML. You could take several existing models, and add together the elements into a new file. (We'd also love to have the model in our repository, if you would like to make a pull request with the model and some unit test afterwards, that would be great!) For the base aeif model: https://github.com/nest/nestml/blob/master/models/neurons/aeif_cond_alpha_n… For the beta kernel: https://github.com/nest/nestml/blob/master/models/neurons/iaf_cond_beta_neu… For multiple input ports: https://github.com/nest/nestml/blob/master/models/neurons/traub_cond_multis… Please note that we are in the process of reviewing/merging a pull request related to refractoriness which could be of relevance to your development, please see https://github.com/nest/nestml/pull/1100 for the new preferred way of implementing absolute refractoriness. We are also working on an "include" statement, that will allow you to include one file (for instance, containing the beta kernel) from another file (the neuron model), making NESTML much more modular. Stay tuned, and please let us know how you fare! With kind regards, Charl On Tue, Oct 8, 2024, at 10:44, tanguy.damart(a)protonmail.com wrote:

Hello everyone, Is there a NESTML version of the NEST model aeif_cond_beta_multisynapse ? (https://nest-simulator.readthedocs.io/en/stable/models/aeif_cond_beta_multi…) If not, is there any difficulties that I might face implementing it in NESTML that I need to be aware of ? (Like how to handle multiple types of synapses). Best, Tanguy _______________________________________________ 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

1:20 p.m.

Hi Tanguy, Sorry for the slightly confusing statement about "handling all presynaptic spikes"; this is reference to a port being able to have an "excitatory" or "inhibitory" qualifier, which is not relevant in your use case. For connecting synapses to the right ports on the neuron, please see the documentation here: https://nestml.readthedocs.io/en/latest/running/running_nest.html#multiple-… Please let us know if you run into any futher issues! With kind regards, Charl On Fri, Oct 11, 2024, at 10:33, Tanguy Damart wrote:

Hi Charl, Thank you for the pointers, I made good progress on the model using the traub_cond_multisyn_neuron.nestml since it has the four synpatic types I was interested in. However, I am still having some troubles with the input ports. I implemented my ports as in the traub model as: """ input: AMPA <- spike NMDA <- spike GABA_A <- spike GABA_B <- spike I_stim pA <- continuous """ But I read in the doc "an unmarked port will by default handle all incoming presynaptic spikes." Does that mean that when creating the connections, I cannot connect to one specific synapse type ? I tried: """ nest.Connect(noise, neuron, syn_spec={"synapse_model": "AMPA"}) """ and """ nest.Connect(noise, neuron, syn_spec={"synapse_model": "static_synapse", "receptor_type": "AMPA"}) """ and both failed. Could you let me know how to proceed ? Cheers, Tanguy On Tuesday, 8 October 2024 at 19:55, Charl Linssen <nest-users(a)turingbirds.com> wrote:

Hi Tanguy, Thanks for writing in! It shouldn't be any problem to implement this neuron using NESTML. You could take several existing models, and add together the elements into a new file. (We'd also love to have the model in our repository, if you would like to make a pull request with the model and some unit test afterwards, that would be great!) For the base aeif model: https://github.com/nest/nestml/blob/master/models/neurons/aeif_cond_alpha_n… For the beta kernel: https://github.com/nest/nestml/blob/master/models/neurons/iaf_cond_beta_neu… For multiple input ports: https://github.com/nest/nestml/blob/master/models/neurons/traub_cond_multis… Please note that we are in the process of reviewing/merging a pull request related to refractoriness which could be of relevance to your development, please see https://github.com/nest/nestml/pull/1100 for the new preferred way of implementing absolute refractoriness. We are also working on an "include" statement, that will allow you to include one file (for instance, containing the beta kernel) from another file (the neuron model), making NESTML much more modular. Stay tuned, and please let us know how you fare! With kind regards, Charl On Tue, Oct 8, 2024, at 10:44, tanguy.damart(a)protonmail.com wrote:

Hello everyone, Is there a NESTML version of the NEST model aeif_cond_beta_multisynapse ? (https://nest-simulator.readthedocs.io/en/stable/models/aeif_cond_beta_multi…) If not, is there any difficulties that I might face implementing it in NESTML that I need to be aware of ? (Like how to handle multiple types of synapses). Best, Tanguy _______________________________________________ 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
Tanguy Damart
tanguy.damart＠protonmail.com