NEST Users June 2022

users@nest-simulator.org

13 participants
16 discussions

回复：Re: About the Izhikevich model
by jcye 10 Jun '22

10 Jun '22

Dear Professor Hans Ekkehard， Thank you for your answer, which gives me a deeper understanding of Izhikevich model. There is a delay when firing a spike between neurons. If there is an refractory period, can I think that only one spike will be sent in this delay interval. Best wishes, Chao. ------------------ 原始邮件 ------------------ 发件人: "NEST User Mailing List" <hans.ekkehard.plesser(a)nmbu.no>gt;; 发送时间: 2022年6月10日(星期五) 下午4:57 收件人: "NEST User Mailing List"<users(a)nest-simulator.org>gt;; 主题: [NEST Users] Re: About the Izhikevich model   Hi Chao,   In real neurons, the refractory period arises from a combination of biophysical mechanisms. After firing an action potential, the cell needs to recover before it can fire another one. In simplified neuron models, such as most integrate-and-fire models, which do not include these recovery mechanisms, one usually adds an explicit refractory period to capture the effect of the biophysical recovery mechanisms in a mathematically or computationally simple way.   But if a neuron model includes (slow) recovery variables that will prevent it from spiking for some period after firing a spike, adding an explicit refractory period may not be required. Izhikevich decided that this was the case for his model, and thus there is no explicit refractory period that could be set as a parameter. The neuron model has its refractoriness simply "built in", with details depending on the parameters.   Best regards, Hans Ekkehard   --   Prof. Dr. Hans Ekkehard Plesser Head, 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 Home http://arken.nmbu.no/~plesser       On 10/06/2022, 09:31, "jcye" <jc.ye(a)foxmail.com> wrote:   Some people who received this message don't often get email from jc.ye(a)foxmail.com. Learn why this is important   Dear NEST Community,   When I use NEST, I find that Izhikevich model has no refractory period. Whether there is a specific reason for this setting or whether the model itself does not have this refractory period? After all, according to my understanding, all neurons in biology have the characteristics of refractory period. I would be happy to get any feedback on it. Thanks, Chao.

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Free registration is now open for CNS*2022 satellite tutorials: June 27--July 1
by Ankur Sinha 08 Jun '22

08 Jun '22

Dear all, Apologies for the cross-posts. The INCF/OCNS Software Working Group is happy to announce that the schedule for the CNS*2022 satellite tutorials from June 27--July 1 has now been published here: https://ocns.github.io/SoftwareWG/pages/software-wg-satellite-tutorials-at-… Free registration is also now open at: https://framaforms.org/incfocns-software-wg-cns2022-satellite-tutorials-reg… To prevent spam/zoom crashing, links to zoom meetings for the tutorial sessions will be limited to registrants only. Therefore, while registration is free, it is required. The satellite tutorials feature sessions on: - Arbor - Brian2 - Introduction to containers - EBRAINS - GeNN - Keras/TensorFlow - LFPy - MOOSE - Neo + Elephant - NEST - NetPyNE - NeuroLib - NeuroML - NEURON - OSBv2 - RateML Please spread the word, and we look forward to seeing you there! -- Thanks, Regards, Ankur Sinha (He / Him / His) | https://ankursinha.in Research Fellow at the Silver Lab, University College London | http://silverlab.org/ Free/Open source community volunteer at the NeuroFedora project | https://neuro.fedoraproject.org Time zone: Europe/London

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No NEST Developer Video Conference (Pentecost)
by Dennis Terhorst 06 Jun '22

06 Jun '22

Dear NEST Users & Developers! Due to the Pentecost holidays in many countries following the Gregorian calendar we skip today's meeting. Our next fortnightly Open NEST Developer Video Conference will be in two weeks on Monday June 20, 11.30-12.30 CEST (UTC+2). Looking forward to seeing you again 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 dry_run
by 512491013＠qq.com 03 Jun '22

03 Jun '22

Dear all, In the paper“The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code”(2017), I found an article about the description of NEST Dry-run Mode, which I am very interested in. However, I don't seem to find relevant information about how to use dry-run in the document. May I ask if there are any relevant examples of using dry-run? best, Cong

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Re: Nest 3.3
by Steffen Graber 01 Jun '22

01 Jun '22

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I can not install Nest 3.3 simulator in Ubuntu 18.04
by salvatore.taffara＠phd.unict.it 01 Jun '22

01 Jun '22

Hi to the community, In order to install Nest 3.3 in Ubuntu 18.04 WITHOUTH the Docker, I followed two ways: 1) I downloaded the source zip file from "https://github.com/nest/nest-simulator/tags", then I followed the guide in "https://nest-simulator.readthedocs.io/en/v3.3/installation/linux_install.ht…", in particular the "Installation from source without a virtual Python environment" version. What I obtain is an error in the terminal: salvo@salvo-Aspire-GX-781:~/Downloads/nest-simulator-3.3-build$ cmake -DCMAKE_INSTALL_PREFIX:PATH=/home/nest /home/salvo/Downloads/nest-simulator-3.3-build/ -- Host triple: x86_64-pc-linux -- Target triple: x86_64-pc-linux CMake Error at /usr/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find Python (missing: Python_INCLUDE_DIRS Python_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.8.13", minimum required is "3.8") Call Stack (most recent call first): /usr/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE) /usr/share/cmake-3.23/Modules/FindPython/Support.cmake:3192 (find_package_handle_standard_args) /usr/share/cmake-3.23/Modules/FindPython.cmake:519 (include) cmake/ProcessOptions.cmake:367 (find_package) CMakeLists.txt:129 (nest_process_with_python) -- Configuring incomplete, errors occurred! See also "/home/salvo/Downloads/nest-simulator-3.3-build/CMakeFiles/CMakeOutput.log". See also "/home/salvo/Downloads/nest-simulator-3.3-build/CMakeFiles/CMakeError.log". salvo@salvo-Aspire-GX-781:~/Downloads/nest-simulator-3.3-build$ 2) I also tried to force the following Ubuntu commands to obtain, from the ppa repository, the Nest version that I need (this is the ppa nest site: https://launchpad.net/~nest-simulator/+archive/ubuntu/nest): sudo add-apt-repository ppa:nest-simulator/nest sudo apt-get update sudo apt-get install nest=3.2-0~202202100714~ubuntu18.04.1 But is seems that the only package that is downloaded from this ppa is nest 2.20, in particular: 2.20.1-0~202103121402~ubuntu18.04.1. What can I do to install Nest 3.3 in my Ubuntu 18.04? Best, Salvo

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