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Combining neuron model features
by d.standage＠bham.ac.uk 03 Dec '20

03 Dec '20

Hi all - I'm aiming to run simulations using Izhikevich's neuron model (or another efficient model with spike generation), two dendritic compartments, two glutamate receptor subtypes, and temporal synaptic dynamics. My understanding is that Nest supports the Izhikevich neuron model with instantaneous current injection (i.e. no synaptic dynamics), the iaf_cond_alpha_mc neuron model for multiple compartments, the aeif_cond_alpha_multisynapse model for multiple receptor subtypes, and any of the _psc_ or _cond_ neuron models for synaptic dynamics. Am I looking at multiple choice here? I.e. I can't use a single neuron model with all of these features? If so, does anyone know of any Nest add-ons that efficiently handle all the features above? I'd be grateful for any advice. Best Dominic

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Technical Editor – European Research Infrastructures for Neuroscience (EBRAINS)
by Hans Ekkehard Plesser 03 Dec '20

03 Dec '20

Dear colleagues, The Computational Neuroscience Group at the Norwegian University of Life Sciences (www.nmbu.no<http://www.nmbu.no/>) aims to recruit a technical editor in a senior engineer position. The position is part of our contribution to the Human Brain Project (www.humanbrainproject.eu<http://www.humanbrainproject.eu/>) in building the European EBRAINS research infrastructures for neuroscience. This full-time position is available immediately and limited until 31 March 2023. As technical editor, you will be part of the EBRAINS High-Level Service Team and be responsible for coordinating and supervising the production and provision of documentation and tutorial materials for EBRAINS service offerings with the pertaining EBRAINS partners. We are looking for applicants with a master's, preferably a doctoral, degree in a STEM discipline, ideally with experience in technical writing, documentation generation systems, and neuroscience. Closing date for applications is 4 January 2021. For more information about the position and to submit your application, please see https://www.jobbnorge.no/en/available-jobs/job/196909/technical-editor-seni… Please contact Prof Hans Ekkehard Plesser (hans.ekkehard.plesser(a)nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>) if you have any questions concerning the position. 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<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser

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Reset Spike Detector
by feldotto 03 Dec '20

03 Dec '20

Dear all,I am running a large simulation where I need to evaluate the spike frequency of large populations in several elapsed time frames. In order to keep this procedure efficient and memory efficient, is it possible to reset the spikeDetector (delete all events)?Thanks in advance!Best,Benedikt

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Getting single neuron spiking
by nosratullah mohammadi 30 Nov '20

30 Nov '20

Dear NEST Users, I wonder how to get single neuron spikes out of spike detector that record all of the neurons in the network. Best, Nosratullah Mohammadi (Mr.)

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Open NEST Developer Video Conference Monday 23 November 2020 11:30 CET (UTC+1)
by Dennis Terhorst 23 Nov '20

23 Nov '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 23 November, 11.30-12.30 CET (UTC+1). 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 For the in-depth discussion the topic of "/Compiler variants vs. MPI implementations/" was proposed, as this is recently causing headache on some setups. The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-11-23-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 network object
by alehr 20 Nov '20

20 Nov '20

Dear NEST developer, I would like to initialize a network with neurons and connections and then run many simulations with it. It would be great if I could build the network one time and then deepcopy (or something similar) for each simulation. Is something like this possible? Thanks, Andrew Lehr

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Microcircuit example, segmentation fault
by d.standage＠bham.ac.uk 17 Nov '20

17 Nov '20

Hi all - I'm running NEST on Ubuntu 18.04, installed with Conda. I can run the example networks in the user documentation, except the Microcircuit Example (having downloaded all the files). It causes a segmentation fault during the call to Simulate( ). I can provide the full error message, but in the interest of brevity - Signal: Segmentation fault (11) Signal code: Address not mapped (1) ... [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x128a0)[0x7feb38d5f8a0] ... Segmentation fault (core dumped) Has anyone else had this issue? I'd be grateful for any help you can provide. Best Dominic

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Re: NEST on macOS 11 Big Sur
by Joris Dolderer 14 Nov '20

14 Nov '20

Thank you for your very useful e-mail! You wrote a lot, but you also had something to say. On Sat, 14 Nov 2020, 13:35 Hans Ekkehard Plesser, < hans.ekkehard.plesser(a)nmbu.no> wrote: > > Dear all, > > I am happy to report that NEST seems to work find under macOS 11 Big Sur. > So far, I have only tested on Intel hardware, a system with the Apple M1 > chip is on its way. > > Specifcially, I proceeded as follows: > > 1. After upgrading to Big Sur, run "brew doctor" and follow the > instructions to update the Apple Command Line Tools. If you encounter > problems, see > https://stackoverflow.com/questions/64821648/homebrew-fails-on-macos-big-sur > > 2. Run "brew update" and "brew upgrade". > > 3. For safety's sake, I then ran "brew uninstall nest" and then "brew > install nest". This gave me a working NEST 2.20.0 installation. > > > To build NEST myself, I first performed steps 1 and 2 above and then > > 3. conda update conda > conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython > nose > conda activate nest_dev > pip install junitparser > > The nomkl package ensures that NumPy does not use Intel's MKL, which can > lead to conflicting OpenMP libraries. > Junitparser is needed to handle testsuite results and is only available > from PyPI. > > 4. Pull latest sources from NEST master branch to src > > 5. mkdir bld > cd bld > cmake -DCMAKE_INSTALL_PREFIX:PATH=<install path> -Dwith-mpi=ON ../src > make -j4 install && make installcheck > > All tests pass. If many MPI tests fail, you may need to add > --oversubscribe to the mpirun command in your .nestrc file. C++ tests will > only run if you have installed boost, e.g., with "brew install boost". > > 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 > > > _______________________________________________ > NEST Users mailing list -- users(a)nest-simulator.org > To unsubscribe send an email to users-leave(a)nest-simulator.org > > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > 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), Prof. Dr.-Ing. Harald Bolt > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > >

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NEST on macOS 11 Big Sur
by Hans Ekkehard Plesser 14 Nov '20

14 Nov '20

Dear all, I am happy to report that NEST seems to work find under macOS 11 Big Sur. So far, I have only tested on Intel hardware, a system with the Apple M1 chip is on its way. Specifcially, I proceeded as follows: 1. After upgrading to Big Sur, run "brew doctor" and follow the instructions to update the Apple Command Line Tools. If you encounter problems, see https://stackoverflow.com/questions/64821648/homebrew-fails-on-macos-big-sur 2. Run "brew update" and "brew upgrade". 3. For safety's sake, I then ran "brew uninstall nest" and then "brew install nest". This gave me a working NEST 2.20.0 installation. To build NEST myself, I first performed steps 1 and 2 above and then 3. conda update conda conda create -n nest_dev nomkl numpy scipy matplotlib ipython cython nose conda activate nest_dev pip install junitparser The nomkl package ensures that NumPy does not use Intel's MKL, which can lead to conflicting OpenMP libraries. Junitparser is needed to handle testsuite results and is only available from PyPI. 4. Pull latest sources from NEST master branch to src 5. mkdir bld cd bld cmake -DCMAKE_INSTALL_PREFIX:PATH=<install path> -Dwith-mpi=ON ../src make -j4 install && make installcheck All tests pass. If many MPI tests fail, you may need to add --oversubscribe to the mpirun command in your .nestrc file. C++ tests will only run if you have installed boost, e.g., with "brew install boost". 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

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Open NEST Developer Video Conference Monday 9 November 2020 11:30 CET (UTC+1)
by Dennis Terhorst 09 Nov '20

09 Nov '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference today Monday 9 November, 11.30-12.30 CET (UTC+1). 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/2020-11-09-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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