November 2021 - NEST Users - NEST Initiative Mail

NESTML: neuron/synapse model with differential dynamics for computing post synaptic currents
by barthelemy 16 Dec '21

16 Dec '21

Dear all, I am a new NEST user. I have a question concerning the range of neuron/synapses model possibilities of NEST. I would like to implement my own neuron/synapse model with NESTML, but I am unsure that it would be possible. Indeed, in my model, synaptic currents are not only relying on pre-synaptic spikes. To compute synaptic currents, the opening probability of pre-synaptic channel receptors are required. Those pre-synaptic channel receptors opening probabilities are evolving according to differential equations involving second order dynamics, with specific decays and taking into account the pre-synaptic spikes arrivals times at this specific synapse. Those differential equations for the opening probabilities are relying on different parameters, according to the neurotransmitter type (GABA A,GABA B, NMDA, AMPA ). Furthermore, additionally to the input spikes and the pre-synaptic channel receptors opening probabilities, the current membrane potential of the post-synaptic neuron is also required to compute the synaptic currents. Do you know if one of the NEST models implement similar dynamics? Is it possible to compute such synaptic dynamics with NESTML by creating a synapse or (and) a neuron model? Or is it not, due to specific limitations? Thank you, Best regards, JB

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NEST v3.1: Missing data for spike_recorder (ascii)
by Maryada Maryada 30 Nov '21

30 Nov '21

Dear NEST users, I am trying to debug my network and I found that my spike_recorder with *ascii* option isn't working as expected. I am simulating a network for a few milliseconds (say 1000. ms) and then do some structure changes and then re-run for another phase of a few ms (say 4000. ms) In the compact version, I am trying to see how this sample code would work. import nest nest.ResetKernel() nest.SetKernelStatus({ "overwrite_files": True, "data_path": './Debug-Log', "data_prefix": 'DEBUG-SPIKE-REC', }) noise_device = nest.Create("poisson_generator",params={'start': 0.,'rate' : 100.}) sd_params = { "record_to": 'ascii', "label": "Input_spike_recorder" } Input_SD = nest.Create("spike_recorder",1, params=sd_params) nest.Connect(noise_device,Input_SD) nest.Simulate(100.) # do something here nest.Simulate(100.) *Issue:* I only get the data recorded from 100th millisecond but for memory, I get all the data from 0-200 ms. This behavior is consistent for both overwrite_files as True and False. In the previous version (v2.20) I also used the same approach and had no issues. Is there a newer way to do such a simulation paradigm? I didn't find anything on this on the comparison page of NESTv2.x and NESTv3.x Am I missing something? It's really important for my work, I hope I could find a solution. -- Thanks and Regards *Maryada*

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FitzHugh-Nagumo model in Nest simulator
by s.taffara92＠gmail.com 29 Nov '21

29 Nov '21

Hi, I visited the page 'https://nest-simulator.readthedocs.io/en/latest/models/' looking for the FitzHugh-Nagumo model keyword. I want to use it to create this kind of neuron in Nest. I can not find it. Can anyone help me? Thanks, Salvo

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Random seed in NEST 3.0
by Maryada Maryada 26 Nov '21

26 Nov '21

Dear NEST users, As I understood from the documentation unless you set the seed using nest.rng_seed, nest.random.normal (for instance) should return the same value nest.ResetKernel() nest.rng_seed = 21#69696 v_m = nest.random.normal(mean=-51., std=10.) v_m.GetValue() In this code, I always receive the same v_m value for both cases, if the seed is set as 21 or 69696. The only time it changes is if I remove ResetKernel() call, which then is expected to return different values irrespective of rng_seed. With this code below, I also got the same results irrespective of rng_seed value nest.ResetKernel() nest.rng_seed = 3333#69696 for _ in range(10): v_m = nest.random.normal(mean=-51., std=10.) print(v_m.GetValue()) So, maybe rng_seed doesn't reflect on nest.random.normal distribution. However, then how can I make sure it draws a different set of values? -- Thanks and Regards *Maryada*

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Trial lecture Luiz Gadelha tomorrow (Thu) 9.00 in Alfa
by Hans Ekkehard Plesser 24 Nov '21

24 Nov '21

Dear all, Just a reminder about Luiz Gadelhas trial lecture tomorrow at 9 in Alfa. Same procedure as before. Oliver and Habib: Will you be available for chats from ca 11.15 on? Then campus tour and lunch from ca 12. Luiz will have to take the 14.30 bus from Korsegården to Gardermoen. Best, 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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Izhikevich Simulation
by Allen Rabayda 22 Nov '21

22 Nov '21

Dear Nest Users, Has anyone used any NEST Synapse Models to create Gamma Rhythms during a simulation with the NEST Izhikevich Neuron model? My simulation, which uses the Stdp-Synapse model (additive type) does not appear to be converging into gamma rhythms (w/bi-model wt distribution) using super-threshold poisson point process (ref: Polychronization Computation With Spikes (Izhikevich, 2006), - DOI: 10.1162/089976606775093882 <https://doi.org/10.1162/089976606775093882>) - - - - Thanks for any suggestions, Best Regards, --Allen

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Open NEST Developer Video Conference Monday 22 November 2021 11:30 CET (UTC+1)
by Dennis Terhorst 22 Nov '21

22 Nov '21

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference, today Monday 22 November, 11.30-12.30 CET (UTC+1). Feel free to join the meeting also just to bring your own questions for direct discussion in the in-depth section. 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/2021-11-22-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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Call for Papers: Reproducibility in Neuroscience
by Alberto Antonietti 19 Nov '21

19 Nov '21

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Installation procedure of NEST on M1 mac
by Julien Ballbé 18 Nov '21

18 Nov '21

Dear Madam, Dear Sir As a starting doctoral student in the field of computational neurosciences, I am particularly interested in using NEST in my research works. However, I am a bit confused about the procedure to install NEST on a M1 macbook pro, therefore, I prefer to ask you before doing anything. From what I understood from your website here are the steps that, I suppose, I should do to install NEST properly: - as I use a M1MAX Mac (MacOS 12.0) , I can't just install nest, I have to build it. To do so: - Download Miniforge for arm64 (from which I will be able to use Conda right?) - Install Python 3.9.4 for arm Mac macOS 64-bit universal2 installer <https://www.python.org/ftp/python/3.9.8/python-3.9.8-macos11.pkg> - Download the nest source code directly from github ( https://github.com/nest/nest-simulator) - Create a conda environment using the following command conda env create -f extras/conda-nest-simulator-dev.yml - Activate this environment ( conda activate...) - Create a build directory outside the NEST source and go into it - Install cmake package using conda ( conda install -c anaconda cmake) - Configure NEST by running: cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir> <nest_source_dir> - Once done I can run make. make install. make installcheck Here are my questions: - Is this installation procedure correct? - Once installed, how can I launch NEST from a python interpreter such as Spyder? Or is it only possible to launch it within a terminal window? - I am quite new to managing packages, so correct me if I am wrong, but have I to install everything using exclusively Conda ? - What is the purpose of creating a new environment to build NEST -Is there anything I missed or misunderstood? I realize how many questions I ask you, and I am very grateful for every advice you could give me. If it is more convenient for you, we can have a phone call when you want. -- *Julien BALLBÉ Y SABATÉ* *Étudiant en thèse - PhD student* *Neurophysiology of Visual Computation* Centre Giovanni Borelli - CNRS UMR 9010 Université de Paris 45 rue des Saint-Pères, 75006 Paris, France Tel: +33 6 79 03 40 35

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[NEST 3.1] autapses/multapses switch for structural plasticity
by Aadhar Sharma 17 Nov '21

17 Nov '21

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NEST Users November 2021