- NEST Users - NEST Initiative Mail

by Alvin Spivey

I'm trying to install and use NEST on google Colab, but it's not importing: !pip install -Uqq nest !pip install -Uqq nestml !pip install -Uqq pysilsub import nest import nestml import numpy as np import matplotlib.pyplot as plt from pysilsub import observers from nestml.network import Network from nestml.models import ConeNakaRushton Am I able to use NEST on Google Colab? -- Alvin J. Spivey, Ph.D. (c) 843.267.8055

1 day, 22 hours

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Open NEST Developer Video Conference Monday April 22, at 11:30 CEST (UTC+0200)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday April 22, 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/2024-04-22-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-04-22-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 ----------------------------------------------------------------------

2 days, 19 hours

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NEST Conference 2024 - Extension of abstract submission deadline

by Hans Ekkehard Plesser

Dear all, The abstract submission deadline for the NEST Conference 2024 has been extended to 30 April. We are looking forward to your contributions! [Image] The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference Important dates 26 April 2024 - Deadline for NEST Initiative membership applications eligible for fee reduction 30 April 2024 - Extended deadline for submission of contributions 08 May 2024 - Notification of acceptance 07 June 2024 - Registration deadline 17 June 2024 - NEST Conference 2024 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- 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

1 week, 1 day

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Enhancement of C++ implementation of DumpLayerConnections()

by Xavier Otazu

Hi! After using some PyNEST functions and modifying the C++ implementation of DumpLayerConnections(), I was thinking on a possible further improvement of this function (or creating a new function). But since I do not know the design and architecture of C++ nestkernel code, I prefer to ask. In my code I normalize the presynaptic connections of every neuron. To do this, I originally do something like for i in range(len(target_layer)) conn[i] = nest.GetConnections(source_layer, target_layer, synapse_model) normalize(conn) Since I am using MPI and the loop iterates over all the neurons, I modified the previous code to local_nodes = nest.GetLocalNodeCollection(target_layer) local_nodes = nest.NodeCollection(local_nodes) for i in range(len(local_nodes)) conn[i] = nest.GetConnections(source_layer, local_nodes, synapse_model) normalize(conn) This last code is faster that the previous one (I guess that local_nodes variable is local to every MPI process and, as a consequence, GetConnections() is more efficient because it only works with local nodes instead of with all of them). Using the idea of the GetLocalNodeCollection(), I was thinking it could be used into the C++ implementation of DumpLayerConnections(). Presently, this function obtain all the connections between source and target layers. Could it be possible to call the equivalent C++ implementation of GetLocalCollection()? I understand that the problem is that, since DumpLayerConnections() needs the spatial information of the layers, the node collections obtained with GetLocalNodeCollection() (I guess similarly its C++ implementation) does not have this spatial information. As a second possibility, I was thinking on adding a new method (GetSpatialInformation()) and enhancing DumpLayerConnections() (or add a new function). The GetSpatialInformation() function could return the spatial information of a collection of nodes (the ones obtained by GetLocalNodeCollection() ). The DumpLayerConnections() (or a new function) could be enhanced by changing the target layer parameter to a pair of parameters that contain the local nodes collection and their spatial information. Something like DumpLaterConnections(source_layer, local_nodes_collection, spatial_information, synapse_model). This way DumpLayerConnections() will only used local nodes and would be much faster. Sorry for the technical email. Xavier

2 weeks, 1 day

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NEST Conference 2024 - reminder for abstract submission deadline on 15 April 2024

by Hans Ekkehard Plesser

Dear all, The abstract submission deadline for the virtual NEST Conference 2024 is approaching (15 April 2024). We are looking forward to your contributions! The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will again take place as a virtual conference on Monday/Tuesday 17/18 June 2024. We are inviting contributions to the conference, including talks, "posters" and workshops on specific topics. Important dates 15 April 2024 - Deadline for submission of contributions 26 April 2024 - Deadline for NEST Initiative membership applications eligible for fee reduction 08 May 2024 - Notification of acceptance 07 June 2024 - Registration deadline 17 June 2024 - NEST Conference 2024 starts For more information on how to submit your contribution, register and participate, please visit the conference website https://nest-simulator.org/conference We are looking forward to seeing you all in June! Hans Ekkehard Plesser and the conference organizing committee -- 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

2 weeks, 1 day

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Open NEST Developer Video Conference Monday April 8, at 11:30 CEST (UTC+0200)

by Hans Ekkehard Plesser

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday April 8, 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. Special topic today is the status of the upcoming NEST 3.7 release. 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 * NEST Conference 2024<http://www.nest-initiative.org/conference>: Submission Deadline 15 April 2024 * NEST 3.7 RC1 Status * Reduce number of warnings (see, e.g., https://github.com/nest/nest-simulator/actions/runs/8566897766) * Porting tests from SLI to Py The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-03-25-Open-NEST-Developer-… Looking forward to seeing you soon! Cheers, Hans Ekkehard Plesser 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 * 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<tel:+493020097938800> 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 -- 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

2 weeks, 2 days

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Questions regarding the iaf_psc_exp model

by anh.phan＠tuni.fi

Hello, I have some questions regarding the iaf_psc_exp model. When it receives current from a current generator (with static synapse), does that current go to receptor_type 0 and not be filtered through an exponential kernel? Secondly, I would like to confirm if the exponential PSCs follow the exponential function:: i_syn(t) = (q / tau_syn) * exp(-t / tau_syn) * Θ(t) , where Θ(t) is the Heaviside step function defined as Θ(t) = 1 fot t >0 and Θ(t) = 0 otherwise. Additionally, is q chosen to be equal to tau_syn? Thank you very much! Best regards, Anh Phan

3 weeks, 1 day

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Open NEST Developer Video Conference Monday March 25, at 11:30 CET (UTC+0100)

by Dennis Terhorst

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today *Monday March 25, 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. Special topic today is the status of the /upcoming NEST 3.7 release/. 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/2024-03-25-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-03-25-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 ----------------------------------------------------------------------

1 month

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NESTML sample random distributions - assertion failed

by chiara de luca

Dear NESTML community, I have a problem with random number generator in the new version of nestml. Specifically, I am using nest 3.6.0 nestml 7.0 This is what I would like to do: whenever creating a neuron with a set of parameters defined by the user, each parameter should be affected by a "gaussian error" with defined variability. I tried to use the internal random_normal() function but with the current version I am getting some issues there. Specifically, whenever trying to call such function from the "internals", "parameters", "state" blocks the model is correctly generated (no errors returned) but exits with en error whenever trying to "install". The error is the following Assertion failed: (tid < static_cast< size_t >( vp_specific_rngs_.size() )), function get_vp_specific_rng, file my/path/to/miniforge3/conda-bld/nest-simulator_1707218961774/work/nestkernel/random_manager.h, line 173. [1] 32875 abort python test.py Such problem does not exist for random_normal() called within the update and equations blocks. Attached some minimal code to reproduce the error. Best, Chiara

1 month

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DumpLayerConnections() enhancement request

by Xavier Otazu

Hi! I am using DumpLayerConnections() with two layers with around 100x100 nodes each layer. Every layer node is connected to around 100 nodes on the other layer. Calling the DumpLayerConnections() takes around 10-15 minutes to save connections to file. I know it is a too general request, but it would be nice if this function is faster. In my particular case, I obtain these connections in a previous step using GetConnections(). I guess (hence I am probably wrong) that DumpLayerConnections() calls GetConnections(). If I am right, I believe it could be an interesting enhancement to implement a DumpLayerConnections() function with input parameters that are a set of connections, that is, something like: myconn = nest.GetConnections(layer1, layer2, ...) nest.DumpLayerConnections(myconn) Thanks a lot in advance! Xavier

1 month, 1 week

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