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How to stimulate neurons in a network with different amplitudes
by Daphne Cornelisse 22 Feb '20

22 Feb '20

Dear nest community, I have a network of 'iaf_cond_alpha' neurons and want to use the 'dc_generator' to apply two different current amplitudes to the network. (see code below) - A subset of the neurons should receive a sub-threshold amplitude so that they won't spike. - A subset of the neurons should receive a suprathreshold amplitude, making them spike. I created a random number of indices of neurons that should receive a suprathreshold current, the rest of the neurons should receive the subthreshold current. However, there doesn't seem any way to set the current amplitude to a subset of neurons. I have looked at all the examples using the dc_generator but couldn't find anything about it. How can this be done? Is it possible? If it's not possible could you point me to the source code so I could potentially write a something for it? Thank you. Kind regards, Daphne *=== code ===* np.random.seed(0) # for reproducibility # amplitudes Asub = 300.6 Asupra = 367.4 # list of all neurons neuron_idx_lst = np.arange(0,N_total) # create random array, these are the neurons that should be stimulated with supra Amplitude supra_indices = np.random.randint(1, N_total, size=int(N_total/neuron_groups-1)) # the rest should receive sub threshold current sub_indices = np.setdiff1d(neuron_idx_lst,supra_indices) # here is where it goes wrong nest.SetStatus(dc_gen[supra_indices], params={'amplitude':Asupra, 'start':stim_start, 'stop':stim_end}) nest.SetStatus(dc_gen[sub_indices], params={'amplitude':Asub, 'start':stim_start, 'stop':stim_end}) >>> TypeError: tuple indices must be integers or slices, not tuple

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Re: Multi-compartmental models
by Benedikt Rank 20 Feb '20

20 Feb '20

Dear Charl, thank you for the specific pointers. This sounds very promising! Best, Benedikt

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Re: Multi-compartmental models
by Benedikt Rank 20 Feb '20

20 Feb '20

Dear Charl, thank you for the specific pointers. This sounds very promising! Best, Benedikt ⁣

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NEST3 is now the Master Branch
by Hans Ekkehard Plesser 20 Feb '20

20 Feb '20

Dear NEST Developers and Users! After more than two years of intense work, NEST 3 is sufficiently close to completion that we merged the nest-3 branch into the NEST master branch in Github yesterday, closing a large number of issues in the process. What does this mean for you? If you are a NEST User, you can continue to use an existing NEST release for now, ideally NEST 2.20.0, the most recent release. If you are a NEST User and feel just a little adventurous, or are a developer, we encourage you to get the newest version of NEST from Github and adapt you model scripts to NEST3. You will find informations about what changed here: https://nest-simulator.readthedocs.io/en/nest-3/guides/from_nest2_to_nest3.… https://nest-simulator.readthedocs.io/en/nest-3/ref_material/nest2_vs_3.html We very much look forward to hear about your experiences with NEST 3 (the good and the not so good ones), so that we can fix any remaining problems before releasing NEST 3.0. Please file bug reports as Github issues. Best, Hans Ekkehard ps: For our colleagues with the HBP and Partnering Projects: We have a session on NEST 3 at the HBP Summit, Wednesday 15.30 in MC3.4. We also have a poster. -- Prof. Dr. Hans Ekkehard Plesser Head, Data Science Section 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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Multi-compartmental models
by benediktr＠hotmail.de 19 Feb '20

19 Feb '20

Dear nest developer, Is there a pre-implemented nest model allowing multiplicative aggregation of compartments/dendritic branches. I am looking for a model that will allow multiplicative aggregation of two dendritic branches at the soma. I very much appreciate any support provided. Best regards, Benedikt

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nest::BadProperty error that behaves like a OOM error
by angpap＠kth.se 17 Feb '20

17 Feb '20

Hello, I am fairly new to NEST and I have been struggling with the following issue. Github repo: https://github.com/angpapadi/wm-net My simulation code consists of 3 python files: - sim.py, the main simulation script, where the model is built and the simulation program is specified - helpers.py a collection of helper functions - parameters.py a script where all parameters are specified. In order to be able to run the code successfully, I have to set certain parameters to unrealistic values. If I try to move any of these parameters towards a more realistic regime, NEST crashes (see end of post for full error message). Most relevant is the fact that setting these parameters to more reasonable values, increases by a lot the amount of spikes that NEST has to keep track of. Examples of such parameters that currently have wrong values: > the DOWNSCALE_FACTOR, that essentially controls the neural network's size. Right now my network size is downscaled 95% of what I would want it to be. There are 2 hypercolumns with 4 minicolumns each. Each minicolumn consists of 4 neurons. > E_rev is a list of the reversal potential for each synaptic port. My neuron model has 3 synaptic ports for AMPA, NMDA and GABA, in that order. The Erev for GABA is correctly set but for AMPA and NMDA I cannot get it to work for values bigger than -25, when the correct reversal potential for both is 0. I cannot find the issue with my code, if there is any. When the simulation is very limited (the aforementioned parameters are set to unrealistic values), the code runs flawlessly and produces the expected plots and spike rasters. Also, if I allocate more resources by running on multiple mpi processes, I can be slightly closer to the correct parameter ranges before the nest::badproperty error occurs. To reproduce the error: 1. You can optionally first run the code as is to verify that it works (by running the sim.py script) 2. Then try setting one of the parameters mentioned above to a more plausible value. You can do so by going to the parameters.py file and either reducing the DOWNSCALE_FACTOR parameter (line 7) or increasing the first two entries of the E_rev list (line 203) that correspond to the AMPA and NMDA reversal potentials, or doing both if you 're feeling adventurous! The error is the following: terminate called after throwing an instance of 'nest::BadProperty' what(): BadProperty [59eb791543aa:00113] *** Process received signal *** [59eb791543aa:00113] Signal: Aborted (6) [59eb791543aa:00113] Signal code: (-6) [59eb791543aa:00113] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7f2c117b7f20] [59eb791543aa:00113] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xc7)[0x7f2c117b7e97] [59eb791543aa:00113] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x141)[0x7f2c117b9801] [59eb791543aa:00113] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8c957)[0x7f2c0a55a957] [59eb791543aa:00113] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x92ab6)[0x7f2c0a560ab6] [59eb791543aa:00113] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x91b19)[0x7f2c0a55fb19] [59eb791543aa:00113] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(__gxx_personality_v0+0x2a8)[0x7f2c0a560488] [59eb791543aa:00113] [ 7] /lib/x86_64-linux-gnu/libgcc_s.so.1(+0x10613)[0x7f2c0d6f1613] [59eb791543aa:00113] [ 8] /lib/x86_64-linux-gnu/libgcc_s.so.1(_Unwind_Resume+0x125)[0x7f2c0d6f1e95] [59eb791543aa:00113] [ 9] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest20EventDeliveryManager18gather_spike_data_INS_9SpikeDataEEEviRSt6vectorIT_SaIS4_EES7_+0x10ed)[0x7f2c0af0684d] [59eb791543aa:00113] [10] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(+0xf4894)[0x7f2c0aee4894] [59eb791543aa:00113] [11] /usr/lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x3f)[0x7f2c08d79ecf] [59eb791543aa:00113] [12] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager7update_Ev+0x151)[0x7f2c0aee0f61] [59eb791543aa:00113] [13] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager12call_update_Ev+0x5a5)[0x7f2c0aee1915] [59eb791543aa:00113] [14] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager3runERKNS_4TimeE+0x1d3)[0x7f2c0aee6713] [59eb791543aa:00113] [15] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest17SimulationManager8simulateERKNS_4TimeE+0x1c)[0x7f2c0aee699c] [59eb791543aa:00113] [16] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZN4nest8simulateERKd+0xc2)[0x7f2c0aecb972] [59eb791543aa:00113] [17] /opt/nest/lib/python3.6/site-packages/nest/../../../libnestkernel.so(_ZNK4nest10NestModule16SimulateFunction7executeEP14SLIInterpreter+0x43)[0x7f2c0ae97a53] [59eb791543aa:00113] [18] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x43)[0x7f2c0a8e9063] [59eb791543aa:00113] [19] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter8execute_Em+0x222)[0x7f2c0a8e6d42] [59eb791543aa:00113] [20] /opt/nest/lib/python3.6/site-packages/nest/../../../libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x7f2c0a8e72be] [59eb791543aa:00113] [21] /opt/nest/lib/python3.6/site-packages/nest/pynestkernel.so(+0x29ac8)[0x7f2c0c5caac8] [59eb791543aa:00113] [22] python[0x50a94c] [59eb791543aa:00113] [23] python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9] [59eb791543aa:00113] [24] python[0x509d48] [59eb791543aa:00113] [25] python[0x50aa7d] [59eb791543aa:00113] [26] python(_PyEval_EvalFrameDefault+0x449)[0x50c5b9] [59eb791543aa:00113] [27] python[0x508245] [59eb791543aa:00113] [28] python[0x589471] [59eb791543aa:00113] [29] python(PyObject_Call+0x3e)[0x5a067e] [59eb791543aa:00113] *** End of error message *** Let me know if you need any additional information and I thank you for your time Angeliki

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Open NEST Developer Video Conference Monday 17 February 2020 11:30 CET (UTC+1)
by Dennis Terhorst 17 Feb '20

17 Feb '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 17 February, 11.30-12.30 CET (UTC+1). For details how to log in see below. As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-02-17-Open-NEST-Developer-… Agenda * Welcome * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues 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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Neuron Model for a Generalized LIF Neuron (No alpha or exponential shaped psc)
by shanka19＠purdue.edu 14 Feb '20

14 Feb '20

Hello NEST Users, I wanted to create a neural network with generalized LIF Neurons. I do not want any exponential or alpha shaped PSCs. Since I cannot draw to describe its shape, I am posting a link from google images to help understand what I mean by a generalized LIF. https://www.google.com/url?sa=i&url=https%3A%2F%2Fwww.researchgate.net%2Ffi… Thanks in advance!

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Realtime access to spikes in simulation
by Benjamin Staude 04 Feb '20

04 Feb '20

Hi NEST-Team, To use the NEST-Simluator in an interactive installation, I would need to 1) have access to the spike in the network in realtime, and 2) send signals (spikes) to neurons in the simulation in realtime. For 1), I could imagine writing the spike-times to a file and then reading that file while the simulation is running. However, I currently don’t see an option for 2). Then I heard that you are actually working on module that would enable realtime I/O-access. Is that the case? And, if so, is there a timeline? Best, Benjamin -- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude(a)gmail.com

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Stop Printing Simulation Details on Terminal (NEST)
by shanka19＠purdue.edu 04 Feb '20

04 Feb '20

Hi, I wanted to know how to stop printing the simulation details on my terminal window. For instance I can see the number of open mpi process, simulation time being printed every time I run a model. I do not want to see the details on my terminal screen, is there a way to do it?

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