February 2025 - NEST Users - NEST Initiative Mail

Exponential Euler Support in NESTML
by justin.r.davis＠essie.ufl.edu 05 Mar '25

05 Mar '25

I've got a version of the HH model (via a NESTML file) which seems to be requiring an exponential Euler solver (ie the one commonly used for e^x dependent biologic systems) to most efficiently solve the equations*. From my reading of the NESTML code generator tools source, only rk45 and forward-Euler are supported. The difference between Euler and Exponential Euler doesn't seem that significant, so I wanted to see if I could get the exponential version implemented....however, what's become unclear to me is whether or not this is a limitation of NEST, NESTML or the underlying solvers and how I'd go about getting a different solver implemented. Are there any guides around on how one would implement a new solver and/or information which would help me figure this out. thx. jrd *=forward Euler does work for some (might work with even smaller timestep) cases, but it requires a time step of 0.01ms. I'm comparing with a Brian2 version of the model running with a 0.1ms time step with it's natively supported exponential Euler solver which is what is making me look into other solvers for my NESTML-based code.

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Open NEST Developer Video Conference Monday February 24, at 11:30 CET (UTC+0100)
by Dennis Terhorst 24 Feb '25

24 Feb '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 24, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-02-24-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-02-24-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 <https://conf.dfn.de/webapp/conference/97938800> * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you’re in. In case you see a dfnconf logo and the phrase “Auf den Meetingveranstalter warten”, just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. * Using the H.323 protocol (eg Polycom): |vc.dfn.net##97938800| or |194.95.240.2##97938800| * Using the SIP protocol:97938800@vc.dfn.de <mailto:97938800@vc.dfn.de> * By telephone: |+49-30-200-97938800| For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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export NEST_MLMODULES=nestmlmodule breaks nest
by Chris Huyck 14 Feb '25

14 Feb '25

I've been using nestml with pynn and nest for some time. I think I built a new model (combining a synapse and a neuron) and it broke nest. So, I can start an environment that has nest, and run nest (sli), pynest and pynn files with nest. However, if I export NEST_MLMODULES=nestmlmodule it breaks nest (sli). That is, I invoke nest, and it says it can't find nestmlmodule. However, if I start a new shell, and do not export NEST_MLMODULES I can run python, import nest, then nest.Install("./nestmlmodule") # in the right directory neuron = nest.Create("iaf_cond_beta_neuron") If I then export NEST_MLMODULES=nestmlmodule I can't import nest from python. Somewhere in the middle of all this, I reran nestml to create just the iaf_cond_beta_neuron, so that's the library I'm using. I'm pretty sure that library works fine. Any idea how to fix it? -Chris From: Chris Huyck <C.Huyck(a)mdx.ac.uk> Sent: 31 January 2025 12:10 To: NEST User Mailing List <users(a)nest-simulator.org> Subject: [NEST Users] Re: nestml synapses in pyNN 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(a)turingbirds.com<mailto:nest-users@turingbirds.com>> Sent: 23 July 2024 11:25 To: users(a)nest-simulator.org<mailto:users@nest-simulator.org> Subject: [NEST Users] Re: nestml synapses in pyNN You don't often get email from nest-users(a)turingbirds.com<mailto:nest-users@turingbirds.com>. Learn why this is important<https://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(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>

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nestml synapses in pyNN
by Chris Huyck 14 Feb '25

14 Feb '25

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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nestml doesn't work on synapse models
by Chris Huyck 12 Feb '25

12 Feb '25

I've got a new conda environment. I compile nest (3.7) from a tarball and it runs. I pip install pyNN I pip install nestml (which now gives me nestml8.0.0. Is there some way to tell the version without just uninstalling it?) The neuron models work. The synapse models fail to nestml I tried my models, but went to the noisy_synapse and static_synapse models (from git) Both fail in nest_code_generator.py line 267 (variables_special_cases = ...) Any thoughts about how to get synapses to work in nestml? -Chris

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wrong results eprop examples
by Xavier Otazu Porter 11 Feb '25

11 Feb '25

Hello, I have downloaded several of the eprop python examples, and none of them generate the correct results. For example, the handwritten example, generates a rather random result (the red points data) that do not fit with the expected results. The sinus generation, also generates wrong results. If you want, I can send a small image (not did it now to avoid image spamming). I am using NEST 3.8 with python 3.9 in a linux Rocks enviornment, and python 3.11 in a FreeBSD environment. Thanks a lot in advance. Xavier Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>

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`tsodyks_synapse` and `tsodyks2_synapse` models have different behavior for short term depression
by Pavel Haman 10 Feb '25

10 Feb '25

Hello, I have followed the example script comparing `tsodyks_synapse` and `tsodyks2_synapse` models, which can be found here: https://nest-simulator.readthedocs.io/en/stable/auto_examples/evaluate_tsod… Using the parameter set for depression instead of facilitation I found that `tsodyks2_synapse` model leads to weird peaks of synaptic currents (at least I would not expect that for short term depression) - during the second stimulation the weight rescaling seems to be shifted by one spike compared to tsodyks_synapse (as if parameter "u" would be updated after rescaling the weight instead of before). Does anybody know why is there this difference between the two synapse models? Thank you. All the best, PH

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Building a nest simulation for mnist dataset
by Aditya Srivastava 10 Feb '25

10 Feb '25

I have built a nest simulation for a binary dataset where we have two classes normal and anomalous . So i tried to built a model iun such a way so that the model learns to produce no spike in case of a normal data but when it sees a anomalous data it is producing the spikes. So this model was working fine. Now I am trying to move forward with it and try it on image dataset where I am using simple MNIST data and I have just taken image for one digit and trying to build a same kind of architecture where it should produce almost no spike when it sees a digit one and oin case of other digits it should produce spikes but I am facing issues in it . The model is not able to produce enough spikes and when I am creating more exc connections then spikes are not reducing with each epochs so can you please suggest me a better approach or some suggestion for my current approach. # loading dataset from sklearn.datasets import fetch_openml import numpy as np def preprocess_mnist_digit(digit=1): """ Load and preprocess the MNIST dataset to only include images of a specific digit. Normalize pixel values by dividing by 4 and flatten images. Args: digit (int): The digit to filter (e.g., 1 for digit '1'). num_samples (int): Number of samples to retain. Returns: flattened_images (array): Flattened MNIST images of the specified digit. labels (array): Corresponding labels. """ # Load MNIST data mnist = fetch_openml('mnist_784', version=1) data, labels = mnist['data'], mnist['target'].astype(int) # Convert labels to integers # Filter images that correspond to the specified digit digit_indices = np.where(labels == digit)[0] # Get indices where label is equal to the specified digit # Extract the corresponding images and labels filtered_images = data.iloc[digit_indices].to_numpy(dtype=float) / 4.0 # Normalize filtered_labels = labels[digit_indices] return filtered_images, filtered_labels # Load only images of the digit '1' images, labels = preprocess_mnist_digit(digit=1) # building simulation nest.ResetKernel() # Simulation parameters dt = 0.01 # Simulation time step in ms nest.SetKernelStatus({"resolution": dt}) N = 784 # Number of neurons images=images[:10] gmax = 3 neuron_params = { "tau_m": 140.0, # Membrane time constant in ms "E_L": -70.6, # Resting potential (in mV) "V_th": -40.4, # Threshold potential (in mV) "V_reset": -70.6, # Reset potential (in mV) "V_m":0.0, } nest.CopyModel("stdp_synapse", "stdp_synapse_exc", {"weight":gmax,"alpha":1,"Wmax":gmax, "tau_plus": 20.0,"lambda": -0.0005, "mu_minus": 0, "mu_plus": 0}) nest.CopyModel("stdp_synapse", "stdp_synapse_inh", {"weight":-gmax/(N-1),"alpha":1,"Wmax":-gmax, "tau_plus": 20.0,"lambda": 0.005, "mu_minus": 0, "mu_plus": 0}) G_spike_gen = nest.Create("poisson_generator",N) G_input = nest.Create("parrot_neuron", N) input_spike_recorder = nest.Create("spike_recorder",N) nest.Connect(G_input, input_spike_recorder,"one_to_one") G_hidden = nest.Create("iaf_psc_delta", N,params=neuron_params) G_output = nest.Create("iaf_psc_delta", 1,params=neuron_params) hidden_spike_recorder = nest.Create("spike_recorder",N) nest.Connect(G_hidden, hidden_spike_recorder,"one_to_one") S_in = nest.Connect(G_spike_gen, G_input, "one_to_one") # Connect input to hidden layer with excitatory STDP synapses S_exc = nest.Connect(G_input, G_hidden,"one_to_one",syn_spec = "stdp_synapse_exc") # Retrieve the neuron IDs for G_input and G_hidden input_ids = G_input.tolist() hidden_ids = G_hidden.tolist() # Get the existing excitatory connections and extract their source-target ID pairs exc_connections = nest.GetConnections(G_input, G_hidden) exc_connection_pairs = set(zip(exc_connections.get("source"), exc_connections.get("target"))) for i in input_ids: for h in hidden_ids: if (i, h) not in exc_connection_pairs: nc1 = nest.NodeCollection([i]) nc2 = nest.NodeCollection([h]) nest.Connect(nc1, nc2, syn_spec= "stdp_synapse_inh") S_out = nest.Connect(G_hidden, G_output,"all_to_all",syn_spec = {"weight": 40.4/N}) # training function def train_net(images, spike_tol=0): output_spike_recorder = nest.Create("spike_recorder") output_membrane_recorder = nest.Create("voltmeter", 1) nest.Connect(G_output, output_spike_recorder) # Record output layer spikes nest.Connect(output_membrane_recorder, G_output, "one_to_one") while True: for image in images: for i in range(784): G_spike_gen[i].rate=image[i] nest.Simulate(500) for i in range(784): spikes = nest.GetStatus(hidden_spike_recorder[i], "events")[0] # if length of spikes is not zero then print the number of spikes and the times of spikes also print the index of the input_spike_recorder if len(spikes["times"]) != 0: print("Number of spikes in hidden_spike_recorder",i,":", len(spikes["times"])) print("Times of spikes in hidden_spike_recorder",i,":", spikes["times"]) print("\n") output_spikes_num = len(output_spike_recorder.get()["events"]["times"]) print("# of output spikes: " + str(output_spikes_num)) # del recorder_for_epoch if output_spikes_num <= spike_tol: print("Training finished") break return output_membrane_recorder, output_spike_recorder v, spk = train_net(images, spike_tol = 2) ___________________________________________

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Open NEST Developer Video Conference Monday February 10, at 11:30 CET (UTC+0100)
by Dennis Terhorst 10 Feb '25

10 Feb '25

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday February 10, at 11:30 CET (UTC+0100).* As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams. Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2025-02-10-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2025-02-10-Open-NEST-Developer-…> Looking forward to seeing you soon! Cheers, Dennis Terhorst Log-in information We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (Deutsches Forschungsnetz). You can use the web client to connect. We however encourage everyone to use a headset for better audio quality or even a proper video conferencing system (see below) or software when available. Web client * Visit https://conf.dfn.de/webapp/conference/97938800 <https://conf.dfn.de/webapp/conference/97938800> * Enter your name and allow your browser to use camera and microphone * The conference does not need a PIN to join, just click join and you’re in. In case you see a dfnconf logo and the phrase “Auf den Meetingveranstalter warten”, just be patient, the meeting host needs to join first (a voice will tell you). VC system/software How to log in with a video conferencing system, depends on you VC system or software. * Using the H.323 protocol (eg Polycom): |vc.dfn.net##97938800| or |194.95.240.2##97938800| * Using the SIP protocol:97938800@vc.dfn.de <mailto:97938800@vc.dfn.de> * By telephone: |+49-30-200-97938800| For those who do not have a video conference system or suitable software, Polycom provides a pretty good free app for iOS and Android, so you can join from your tablet (Polycom RealPresence Mobile, available from AppStore/PlayStore). Note that firewalls may interfere with videoconferencing in various and sometimes confusing ways. For more technical information on logging in from various VC systems, please see http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4> -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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Invitation to EBRAINS events in Heidelberg from 12-13 March
by Dennis Terhorst 10 Feb '25

10 Feb '25

Hi everyone, I would like to forward the invitation to the EBRAINS events in Heidelberg next month. Many experts of tools will be there including quite a number of NEST users and developers. You have the opportunity to join tutorials, learn about more interesting tools and directly exchange experience with others. Have a look! --- Dear NEST Community, We are delighted to invite you to join us in Heidelberg, Germanyat theEINC <https://einc.eu/>, from 12-13 March 2025, for a series of EBRAINS events. On*Wednesday,**12 March*, we will host an*EBRAINS Tutorials and Users Day*. It is aimed at both newcomers and experienced users of EBRAINS tools. Newcomers will have the chance to explore the wide range of Open Science Tools and Services available on the research infrastructure, while seasoned EBRAINS users can dive deeper with advanced tutorials and discuss with developers. You can find out more about the Tutorials and Users Day here:https://www.ebrains.eu/news-and-events/accelerate-your-neuroscience-research-with-ebrains-tutorials-and-users-day-in-heidelberg <https://www.ebrains.eu/news-and-events/accelerate-your-neuroscience-researc…> On*Thursday, 13 March*, we will host an*EBRAINS Developers Day*. It will feature introductions for developers on how to integrate tools and services into the EBRAINS software distribution or to integrate services via EBRAINS (workflows). You can find out more about the Developers Day here:https://www.ebrains.eu/news-and-events/developers-day-2025 <https://www.ebrains.eu/news-and-events/developers-day-2025> If you have any questions, please don't hesitate to contactcommunications(a)ebrains.eu <mailto:communications@ebrains.eu>. We hope to see you in Heidelberg! Kind regards, EBRAINSAISBL --- -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute for Advanced Simulation (IAS-6) Computational and Systems Neuroscience & JARA-Institute Brain Structure-Function Relationships (INM-10) Institute of Neuroscience and Medicine Jülich Research Center, Member of the Helmholz Association 52425 Jülich, Germany http://www.csn.fz-juelich.de/ Phone +49 2461 61-85062 ---------------------------------------------------------------------- Forschungszentrum Jülich GmbH 52425 Jülich Sitz der Gesellschaft: Jülich Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Prof. Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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