- NEST Users - NEST Initiative Mail

Order or Computation
by carriere.maxime93＠gmail.com 08 Aug '24

08 Aug '24

Hello everyone, I am trying to replicate our brain-constrained model to NEST. In our model the computation of the inhibition occurs before the inhibition. I believe it's the other way round in NEST. I was wondering, where the order of computation was implemented in NEST and if that was possible to change it. Best, Maxime

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Open NEST Developer Video Conference Monday July 15, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 24 Jul '24

24 Jul '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 15, at 11:30 CEST (UTC+0200).* 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/2024-07-15-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-15-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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nestml syntax problem
by Chris Huyck 19 Jul '24

19 Jul '24

I was using an old version of nest (3.5) and nestml. Someone sent me a nestml model, and that worked. I wanted to make my own model, but the tutorials had a different format. In particular, it seems like the first line of code in the tutorials start with model, and the old version started with neuron of synapse. So, I thought it was time to upgrade, so installed nest 3.7, and pip-ed nestml. (I also installed PyNN as that's the way I typically work.) When I imported generate_target (through python 3.12), I got the typical PyGSL warning; I think that's because I'm using python 3.12 not 3.11, and I don't think it matters in this case. Then I ran the generate_target and I got an error mismatched input 'model' expecting {newline, 'neuron', 'synapse} I expect there's something like a yacc table that specifies the syntax, and somehow I've got the old syntax. I've tried it with several version of nestml 7.0.2, 7.0.0, 6.0.0 and 5.0.0. I think 5.0.0 had the old syntax. I've tried several models from the library, and the Izhikevich tutorial. Any thoughts about how to fix it? -Chris

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e-prop tutorial missing data file
by Xavier Otazu 04 Jul '24

04 Jul '24

Hi! Looking at the e-prop tutorial (https://nest-simulator.readthedocs.io/en/v3.7/auto_examples/eprop_plasticit…), the chaos_handwriting.txt datafile is needed. Where can I find this file? Thanks a lot in advance! Xavier

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Open NEST Developer Video Conference Monday July 1, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 01 Jul '24

01 Jul '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday July 1, at 11:30 CEST (UTC+0200).* 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/2024-07-01-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-07-01-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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Questions about Neuron Update Mechanism and Spike Event Handling in Source Code
by anh.phan＠tuni.fi 25 Jun '24

25 Jun '24

Hi, I've been trying to read through the source code to understand this, but I'm still having trouble figuring it out. From what I can see, the neurons are updated using a for loop, meaning each neuron is updated one at a time. The update function for each neuron can run for multiple timesteps, but I'm unclear on how its B_.input_buffer_ gets updated while the update function is running. If it doesn't get updated during this process, wouldn't it miss some spike events? Additionally, how does the code ensure that neurons updated one at a time for all simulation steps do not miss any spike events? Thank you for your help! Best regards, Anh Phan

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Developers: Please pull Master to your branches / NumPy 2.0 changes
by Hans Ekkehard Plesser 20 Jun '24

20 Jun '24

Dear Colleagues, This mail is mainly for those of you who contribute to NEST Simulator development. NumPy 2.0, released last Sunday, has some minor changes that broke existing tests and examples. This has now been fixed in the master branch (PRs #3226, #3227). Please pull master into all your branches—otherwise, the testsuite will fail on Github and your contributions cannot be merged. Best, Hans Ekkehard -- Prof. Dr. Hans Ekkehard Plesser Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Open NEST Developer Video Conference Monday June 3, at 11:30 CEST (UTC+0200)
by Dennis Terhorst 09 Jun '24

09 Jun '24

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday June 3, at 11:30 CEST (UTC+0200).* Despite many people attending conferences this week, we will briefly meet to offer attention also to smaller questions or more general topics that you may bring. The Project team round, might however be quite short today. Feel free to join the meeting and bring your own quick questions for direct discussion or just to hear what's going on in and around NEST. 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/2024-06-03-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-06-03-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 Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens ----------------------------------------------------------------------

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NEST Conference 2024 — Register by Friday!
by Hans Ekkehard Plesser 04 Jun '24

04 Jun '24

Dear NEST Users, We are looking forward to an exciting Virtual NEST Conference 2024 on Monday/Tuesday 17./18. June 2024. This years program includes keynotes by Tadashi Yamazaki, University of Electro-Communications, Japan Diversity and inclusion: Distributed simulation of multiple brain and body models in multiple simulators on multiple computers across multiple organizations Benedetta Gambosi, University of Pavia A multiarea model predicts the changes in thalamocortical beta oscillations caused by dopamine depletion in basal ganglia and cerebellum Tobias Gemmeke, RWTH Aachen Accelerated Simulation of Biological Neural Networks Behnam Ghazinouri, Ruhr-Universität Bochum The attractor dynamics of behavioral flexibility in spatial and reversal learning complemented by contributed talks, posters and a workshop Introducing Arbor. For the full program an to register, please see https://nest-simulator.org/conference. Registration deadline is this FRIDAY, 7 June 2024. We are looking forward to seeing you at the NEST Conference 2024! Hans Ekkehard Plesser -- Prof. Dr. Hans Ekkehard Plesser Department of Data Science Faculty of Science and Technology Norwegian University of Life Sciences PO Box 5003, 1432 Aas, Norway Phone +47 6723 1560 Email hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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About example structural plasticity?
by Thanh Binh To 21 May '24

21 May '24

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