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Connection management for huge network
by kusch lionel 20 Oct '21

20 Oct '21

Dear all, In my working group, we are working on the creation of the spiking neural network of human CA1 (4.8 million neurons). We are using a specific function for defining the connection between the neurons. This function gives us 30 billion pairwise connections. We would like to know what the most efficient for the creating the network in NEST 3 using this pairwise connectivity. Thank you in advance for your answer, Kusch Lionel

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Adapt custom models from NEST 2.16 to NEST 3.1
by Daniel Todt 20 Oct '21

20 Oct '21

Hello everyone, I want to adapt two custom models called "global_volume_transmitter" and "dopa_connection" from NEST 2.16 to NEST 3.1. The .cpp and .h files are attached to this email. Is it possible to have the models adapted to NEST 3.1? How could this be done? I hope someone can help me with that. Best regards, Daniel Todt -- Daniel Todt HPC in Neuroscience Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich GmbH Tel.: +49 2461 61 85277 E-Mail: d.todt(a)fz-juelich.de ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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), Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Dennis Asked
by Chris Huyck 12 Oct '21

12 Oct '21

I've recently downloaded a new version of NEST, and I'm trying to make a new synaptic model, but am breaking down in building their default MyModule model. The process onhttps://nest.github.io/nest-simulator/extension_modules<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnest.gith…> says to run bootstrap.sh, but I can't find a bootstrap.sh. Do you have a version you could send me? If not, who can I contact for help (and how)? -Chris

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Open NEST Developer Video Conference Monday 11 October 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 11 Oct '21

11 Oct '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 11 October, 11.30-12.30 CEST (UTC+2). Today we again have two possible topics for the in-depth discussion that you may be interested in: * Plasticity models via NESTML, and * NEST wheels (Python package mechanism). As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and 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. 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/2021-10-11-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (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 * 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 - 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

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Open NEST Developer Video Conference Monday 27 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 27 Sep '21

27 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 27 September, 11.30-12.30 CEST (UTC+2). As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and 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. 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/2021-09-27-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (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 * 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 - 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

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NEST 3.1 is there!
by Dennis Terhorst 15 Sep '21

15 Sep '21

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Open NEST Developer Video Conference Monday 13 September 2021 11:30 CEST (UTC+2)
by Dennis Terhorst 13 Sep '21

13 Sep '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 13 September, 11.30-12.30 CEST (UTC+2). Today we have two topics for the in-depth discussion that you may be interested in. As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing work in the team and 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. Agenda * Welcome * Review of NEST User Mailing List * Project team round * In-depth discussion * Failing assertions #2101 <https://github.com/nest/nest-simulator/issues/2101> * Naming of modules (see nest-connplotter:#2 <https://github.com/nest/nest-connplotter/pull/2>) The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2021-09-13-Open-NEST-Developer-… Looking forward to seeing you soon! best, Dennis Terhorst ------------------ Log-in information ------------------ We use a virtual conference room provided by DFN (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 * 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 - 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

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NEST 3.0: Plot weight matrices example ERROR
by Ing Jyh Tsang 31 Aug '21

31 Aug '21

I think there is an error in https://nest-simulator.readthedocs.io/en/stable/auto_examples/plot_weight_m… * min(E_neurons)and min(I_neurons) should be replace to * min(E_neurons.tolist()) and min(I_neurons.tolist())or some other way to get the right values Suggestion: The file plot_weight_matrices.py just contain a def plot_weight_matrices(E_neurons, I_neurons). If it had a complete code to create nodes, assign weights then plot the weight matrixes, the error could have been caught automatically (CI/CD)? Best, Inton

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Problems after ubuntu installed nest-3.0 built on Aug 24 2021
by Ing Jyh Tsang 31 Aug '21

31 Aug '21

Hi, After my ubuntu upgraded nest. Whenever I run a program it does not seems to identify the nest module. For example, running the twoneuron.py example gives: Traceback (most recent call last): File "twoneurons.py", line 43, in <module> import nest.voltage_trace ModuleNotFoundError: No module named 'nest.voltage_trace' Please solution for this? I tried remove and reinstalling and did not work. I did not try building it. Thanks, Inton

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AttributeError: module 'nest' has no attribute 'SetKernelStatus'
by Alberto 31 Aug '21

31 Aug '21

Hi, suddenly, I am starting having this error. I have both PyNN and Nest installed. If it's more related to the PyNN community, I will forward this message to them, but at this moment I don't know if it's more related to Nest or PyNN side. Maybe some of you have met a similar issue. >>> import pyNN.nest as sim Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/__init__.py", line 18, in <module> from . import simulator File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 261, in <module> state = _State() # a Singleton, so only a single instance ever exists File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 58, in __init__ self.spike_precision = "off_grid" File "/home/alberto/.local/lib/python3.8/site-packages/pyNN/nest/simulator.py", line 114, in _set_spike_precision nest.SetKernelStatus({'off_grid_spiking': True}) AttributeError: module 'nest' has no attribute 'SetKernelStatus' Thanks, Alberto

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