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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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Using GPU's to run NEST simulaton
by Daphne Cornelisse 04 Feb '20

04 Feb '20

Hi NEST-team, I would like to run a simulation of > 1000 neurons, and to make my computing time faster I am looking into how to use parallel computing with NEST. I have seen this <https://www.nest-simulator.org/parallel-computing/> page but I can't seem to find anything about using the cloud (e.g. google cloud, colab etc.) and the use of GPU's. I am quite new to this so it could be I missed something. - Is it possible to use a GPU for the nest simulations? - Are the some resources I could learn from? Thank you! Best, Daphne

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NEST 2.20.0 released / Issue 1394 / NEST 3 to become Master Branch soon
by Hans Ekkehard Plesser 31 Jan '20

31 Jan '20

Dear NEST Users! We are very excited about the release of NEST 2.20.0 earlier today, including 454 commits in 82 pull requests by 25 developers since NEST 2.18.0. NEST 2.20.0 brings a wide range of improvements, including * generalized leaky integrate-and-fire neuron models developed by the Allen Institute (Teeter et al, 2018) * STDP synapses with nearest-neighbor spike paring schemes * improved documentation on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Please see below for a complete list of changes. NEST 2.20.0 is available for download from https://github.com/nest/nest-simulator/releases/tag/v2.20.0 To cite NEST 2.20.0, please refer to the Zenodo entry at https://doi.org/10.5281/zenodo.3605514 WARNING: NEST 2.20.0 is affected by issue #1394<https://github.com/nest/nest-simulator/issues/1394>, which may lead to incorrect results under certain circumstances when simulating very large networks across many MPI processes and threads. Simulations using only MPI parallelism, but no threads, work correctly according to our tests. The same holds for simulations using only thread-parallelism. The issue also affects NEST 2.18.0 and 2.16.0, but not 2.14.0. According to our analysis, in affected simulations, a very small number of connections is not created correctly. This happens under random cirucmstances, so that in one series of tests, out of ten identical simulations, five simulations produced correct results, while the remaining five simulations produced different results. For details, please follow the issue on GitHub. We are currently working hard to identify the cause of this issue and hope to be able to provide a fix soon. The next big step forward in NEST development will be the merge of the nest-3 development branch into the master branch on GitHub. NEST 3 will bring major improvements to the user interface and considerable changes under the hood. Please see 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 for more information on changes to come and modifications required to existing scripts. Best regards, Hans Ekkehard Plesser President, The NEST Initiative ------------------------------------------------ NEST 2.20.0<https://doi.org/10.5281/zenodo.3605514> is the result of 454 commits in 82 pull requests by 25 developers since NEST 2.18.0<https://doi.org/10.5281/zenodo.2605422> which was released on June 7, 2019. This release wraps up the 2.x series of NEST and contains many improvements and bug fixes. Highlights are the addition of the generalized leaky integrate-and-fire neuron models by the Allen Institute<https://portal.brain-map.org/explore/models/glif-single-neuron>, STDP synapses with nearest-neighbor spike pairing schemes and improved documentation, available on Read The Docs<https://nest-simulator.readthedocs.io/en/latest/>. Following is a list of all merged pull requests: Enhancements Models * Add STDP synapses with nearest-neighbor spike pairing schemes<https://github.com/nest/nest-simulator/pull/865> * Add generalized leaky integrate-and-fire (GLIF) neuron models by Allen Institute<https://github.com/nest/nest-simulator/pull/1126> * Add iaf_psc_alpha_ps neuron model<https://github.com/nest/nest-simulator/pull/1169> Installation * Add conda-forge installation documentation for Linux and MacOSX<https://github.com/nest/nest-simulator/pull/1204> * Add Fugaku platform CMake file<https://github.com/nest/nest-simulator/pull/1231> * Clean the build process for the NEST Debian packages<https://github.com/nest/nest-simulator/pull/1316> * Hike minimum required CMake to 3.12 and add support for OpenMP with Apple Clang<https://github.com/nest/nest-simulator/pull/1386> * More informative compiler information in CMake summary<https://github.com/nest/nest-simulator/pull/1403> Documentation * Added initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1206> * Add initial membrane potential options to microcircuit example<https://github.com/nest/nest-simulator/pull/1260> * Add new options for installation and improve instructions for NEST<https://github.com/nest/nest-simulator/pull/1262> * Updated/extended macOS install instructions<https://github.com/nest/nest-simulator/pull/1297> * Update DOI and release buttons in README; add Zenodo reference to NEST 2.18.0<https://github.com/nest/nest-simulator/pull/1314> * Add link on website to new PyNEST templates and update citations<https://github.com/nest/nest-simulator/pull/1351> * Provide guidelines to writing to mailing list in documentation<https://github.com/nest/nest-simulator/pull/1368> Kernel * Introduce time-driven spiking connections<https://github.com/nest/nest-simulator/pull/1160> * Add support for sending secondary events to and from devices<https://github.com/nest/nest-simulator/pull/1244> * Add warning about invalid connection descriptors when new connections are created<https://github.com/nest/nest-simulator/pull/1250> * Use an unsigned data type for thread in spike data<https://github.com/nest/nest-simulator/pull/1308> Infrastructure * Fast static check in Travis CI<https://github.com/nest/nest-simulator/pull/1267> PyNEST * New templates for pynest examples and api<https://github.com/nest/nest-simulator/pull/1139> * Add getattr/setattr to GIDCollection<https://github.com/nest/nest-simulator/pull/1249> * Allow specifying arrays of values in the synapse specification when connecting with fixed_total_number<https://github.com/nest/nest-simulator/pull/1266> * Use shape as argument instead of columns/rows/depth and update topology examples to NEST3<https://github.com/nest/nest-simulator/pull/1287> Bug fixes Models * Fix uninitialized variable in iaf_psc_exp<https://github.com/nest/nest-simulator/pull/1225> * Fix handling of rate change in poisson_generator_ps<https://github.com/nest/nest-simulator/pull/1280> Documentation * Remove spurious brackets from code example in tutorial<https://github.com/nest/nest-simulator/pull/1270> * Fix MUSIC example<https://github.com/nest/nest-simulator/pull/1312> Kernel * Fix multiple definition of rho build complain observed on AArch64 with FCC<https://github.com/nest/nest-simulator/pull/1233> * Fix GetConnections to correctly get connections where the target is a global receiving device<https://github.com/nest/nest-simulator/pull/1251> * Fix logical error in elseif-statements in connect functions<https://github.com/nest/nest-simulator/pull/1254> * Check variables of GSL binomial random generator where they are set<https://github.com/nest/nest-simulator/pull/1299> * Ensure number of connections for fixed total number is properly set<https://github.com/nest/nest-simulator/pull/1367> * Fix MyModule by incorporating modelsmodule refactoring from #1069<https://github.com/nest/nest-simulator/pull/1383> * Avoid segfault when using a weight recorder with a probabilistic synapse<https://github.com/nest/nest-simulator/pull/1402> Infrastructure * Fix cppcheck in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1306> Maintenance Models * Fix namespaces in Hodgkin-Huxley neuron models<https://github.com/nest/nest-simulator/pull/1256> * Make multimeter and voltmeter class names lower case<https://github.com/nest/nest-simulator/pull/1345> Installation * Fix nest_vars in case of undefined PYTHONPATH<https://github.com/nest/nest-simulator/pull/1218> * Cleanup for the K computer specific CMake file for v2.18<https://github.com/nest/nest-simulator/pull/1228> * Fix up dependencies in Ubuntu install instructions<https://github.com/nest/nest-simulator/pull/1230> * Files needed to build Debian packages (.deb)<https://github.com/nest/nest-simulator/pull/1255> * Fix extraction of version number if sources are inside another Git repository<https://github.com/nest/nest-simulator/pull/1362> * Let uninstall of NEST Debian package also delete script in profile.d<https://github.com/nest/nest-simulator/pull/1363> Interpreter * Remove handling of external POSIX signals sent to NEST<https://github.com/nest/nest-simulator/pull/1385> Documentation * Convert topology user manual to ReStructuredText<https://github.com/nest/nest-simulator/pull/1214> * Update links to model directory in docs<https://github.com/nest/nest-simulator/pull/1227> * Documentation update pertaining to maximum line length<https://github.com/nest/nest-simulator/pull/1234> * Fix PyNEST installation instructions<https://github.com/nest/nest-simulator/pull/1240> * Update download page for 2.18 and conda-forge<https://github.com/nest/nest-simulator/pull/1247> * Correct typo in random number documentation<https://github.com/nest/nest-simulator/pull/1268> * Fix PyNEST API generation for documentation using mock<https://github.com/nest/nest-simulator/pull/1274> * Add updated NEST examples to Read The Docs <https://github.com/nest/nest-simulator/pull/1277> * Replace iaf_neuron by iaf_psc_alpha in MUSIC tutorial<https://github.com/nest/nest-simulator/pull/1330> * Autogenerate PyNEST examples from source with sphinx_gallery<https://github.com/nest/nest-simulator/pull/1336> * Update syntax formatting for terms in documentation<https://github.com/nest/nest-simulator/pull/1343> * Fix broken CSS style<https://github.com/nest/nest-simulator/pull/1344> * Update mailing list email address<https://github.com/nest/nest-simulator/pull/1346> * Small typographical updates to user documentation<https://github.com/nest/nest-simulator/pull/1397> Kernel * Refactor registration of models in modelsmodule<https://github.com/nest/nest-simulator/pull/1069> * Increase maximum line length in source code formatting style from 80 to 120<https://github.com/nest/nest-simulator/pull/1177> * Unify coeffarray_as_d and coeffarray_as_uint via union<https://github.com/nest/nest-simulator/pull/1243> * Add missing include of sys/time.h<https://github.com/nest/nest-simulator/pull/1273> * Fix threading issue when connecting<https://github.com/nest/nest-simulator/pull/1276> * Remove spurious thread_local_connectors update<https://github.com/nest/nest-simulator/pull/1333> * Fix rounding issue when setting small resolution<https://github.com/nest/nest-simulator/pull/1356> * Improve information given by error messages typically triggered by Connect<https://github.com/nest/nest-simulator/pull/1399> Infrastructure * Add tests for libnestutil/streamers.h<https://github.com/nest/nest-simulator/pull/1219> * Make version information consistent<https://github.com/nest/nest-simulator/pull/1223> * Update FindLibNeurosim to take Python version into account<https://github.com/nest/nest-simulator/pull/1235> * Remove the remaining markdown config in docs<https://github.com/nest/nest-simulator/pull/1263> * Skip deployment in Travis CI testsuite when not running a build<https://github.com/nest/nest-simulator/pull/1300> * Deploy build artifacts only when the build flag is set in the reply section<https://github.com/nest/nest-simulator/pull/1302> * Change the deployment branch to master<https://github.com/nest/nest-simulator/pull/1304> * Fix cppcheck usage in Travis CI testsuite<https://github.com/nest/nest-simulator/pull/1307> * Switch to GCC8 as default in continuous integration tests on Travis<https://github.com/nest/nest-simulator/pull/1310> * Fix formatting in test_stdp_nn_synapses.py<https://github.com/nest/nest-simulator/pull/1311> * Add security guidelines<https://github.com/nest/nest-simulator/pull/1329> * Moving to Python3.x on OsX<https://github.com/nest/nest-simulator/pull/1335> * Replace Python version by newest available on Travis<https://github.com/nest/nest-simulator/pull/1342> PyNEST * Fix warnings when Cythonizing pynestkernel.pyx<https://github.com/nest/nest-simulator/pull/1322> * Allow installation with Python 3.8<https://github.com/nest/nest-simulator/pull/1340> -- 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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Issue with NEST 2.18.0/python 3.6
by Angeliki Papadimitriou 20 Jan '20

20 Jan '20

Hello, I have an issue regarding random generation in nest version 2.18 with Python3.6. I attach a small python script that replicates my issue (less than 50 lines). In short, I am trying to create two Poisson generators and connect them to the same neuron. I noticed that if I reverse the order by which these Poisson generators are created (using the nest.Create()) function, then I get a different membrane potential response over time. In the code, noise_exc is created before noise_inh. If that order is reversed, the plot is different. My hunch is that this has to do with how nest generates random numbers. So I tried to force the creation of Poisson generators by providing a seed (lines 15 and 18). However this behavior persists. Do you have any insights as to why this happens? At the end of the script (lines 32-43) I provide a trivial case of the desired behavior I am trying to replicate. Thank you for your time Angeliki -- [image: Kth Logo] Angeliki Papadimitriou Research EngineerKTH Royal Institute of Technology *School of Electrical Engineering and Computer Science (EECS)**Division of Computational Science and Technology (CST)* Computational Brain Science Unit Room 4438, Floor 4, Lindstedtsvägen 5 11428 Stockholm, Sweden angpap(a)kth.se <namn(a)kth.se>

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Open NEST Developer Video Conference Monday 20 January 2020 11:30 CET (UTC+1)
by Hans Ekkehard Plesser 19 Jan '20

19 Jan '20

Dear NEST Users & Developers! I would like to invite you to this years first Open NEST Developer Video Conference, tomorrow Monday 20 January, 11.30-12.30 CET (UTC+1). As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-01-20-Open-NEST-Developer-… For details how to log in see below. Agenda * Welcome * Preparing NEST 2.20 release * Preparing merge of nest-3 branch to master * Review of NEST User Mailing List * Review of open Github Pull Request * Review of open Github Issues Looking forward to seeing you soon! Hans Ekkehard Plesser ------------------ 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 _______________________________________________ NEST Users mailing list -- users(a)nest-simulator.org To unsubscribe send an email to users-leave(a)nest-simulator.org

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Segmentation Fault loading custom nest module
by Benedikt Feldotto 17 Jan '20

17 Jan '20

Dear all, I tried to install a custom module into Nest first using the MyModule example as described here https://nest.github.io/nest-simulator/extension_modules The installation works fine without errors, however when I try to load the model into pynest with import nest import('mymodule') I get a "Segmentation fault (core dumped)". The last traceback of debbugging with python pdb is the following: -> engine.run('{%s} runprotected' % decode(cmd)) (Pdb) s --Call-- > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(107)decode() -> def decode(s): (Pdb) s > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode() -> return s.decode('utf-8') (Pdb) s --Call-- > /usr/lib/python2.7/encodings/utf_8.py(15)decode() -> def decode(input, errors='strict'): (Pdb) s > /usr/lib/python2.7/encodings/utf_8.py(16)decode() -> return codecs.utf_8_decode(input, errors, True) (Pdb) s --Return-- > /usr/lib/python2.7/encodings/utf_8.py(16)decode()->(u'(cereb... Install', 26) -> return codecs.utf_8_decode(input, errors, True) (Pdb) s --Return-- > /home/user/.local/lib/python2.7/site-packages/nest/__init__.py(108)decode()->u'(mymod... Install' -> return s.decode('utf-8') (Pdb) s Segmentation fault (core dumped) I already added the model path to my LD_LIBRARY_PATH variable so that the module can be found, but now it cannot be loaded. It looks like a decoding issue, but I don't know what went wrong during the installation. Do you have any idea what could be the issue? I am using python 2.7 and NEST 2.3.1 Thanks! Benedikt Feldotto -- Benedikt Feldotto M.Sc. Research Assistant Human Brain Project - Neurorobotics Technical University of Munich Department of Informatics Chair of Robotics, Artificial Intelligence and Real-Time Systems Room HB 2.02.20 Parkring 13 D-85748 Garching b. München Tel.: +49 89 289 17628 Mail: feldotto(a)in.tum.de https://www6.in.tum.de/en/people/benedikt-feldotto-msc/ www.neurorobotics.net

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NEST Creating a simple network
by shanka19＠purdue.edu 16 Jan '20

16 Jan '20

Hello everyone, Happy New Year! I want to create a simple neural network consisting of a single neuron connected by multiple inputs (spike generators). I am aware that I can create single spike generators and then connect them but it becomes infeasible as the size of input grows. Is there a way to create a network of maybe 100 spike generators connected to a single LIF Neuron without explicitly creating 100 of them? Once the connections are made is there a way that the network is updated when the weights are updated. I want the network to get updated as I update the weights. Now, I update the weights and reset the network to create it again with new weights. Any help would be appreciated. Thanks in advance!

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nest user in nest-docker entrypoint file
by bignamini＠cscs.ch 14 Jan '20

14 Jan '20

Hi all, I have a question about nest user creation/usage in nest docker entrypoint file: I am working with Sarus and Singularity and due to some permission limits I can't create a new user inside a container. I have tried to modify the entrypoint.sh file as follows https://github.com/ChristopherBignamini/nest-docker/blob/no_nest_user_creat… in order to skip the creation of the nest user. I am not a nest expert but everything seems to work, at least if I try to run a couple of examples like one_neuron.py and twoneurons.py. My question is: what is the reason behind the creation and usage of the nest user? Thank you in advance. Cheers Christopher

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Error when compiling MyModule, the example extension module
by eben.cowley42＠gmail.com 10 Jan '20

10 Jan '20

Hi, I'm on Ubuntu 18.10 and I've successfully installed nest to `/usr`. I'm interested in writing my own synapse models and found these instructions for getting started: https://nest.github.io/nest-simulator/extension_modules The configuration step, `cmake -Dwith-nest=/usr/bin/nest-config ../MyModule` works fine. However, when I ran `make` I received the following compiler error: ``` ~/Projects/NEST/MyModule/mymodule.cpp: In member function ‘virtual void mynest::MyModule::init(SLIInterpreter*)’: ~/Projects/NEST/MyModule/mymodule.cpp:128:24: error: no matching function for call to ‘nest::ModelManager::register_connection_model<mynest::DropOddSpikeConnection<nest::TargetIdentifierPtrRport> >(const char [17])’ "drop_odd_synapse" ); ^ In file included from /usr/include/nest/kernel_manager.h:31, from /usr/include/nest/connector_base_impl.h:26, from /usr/include/nest/connection.h:29, from /home/ebanflo/Projects/NEST/MyModule/drop_odd_spike_connection.h:27, from /home/ebanflo/Projects/NEST/MyModule/mymodule.cpp:29: /usr/include/nest/model_manager.h:197:8: note: candidate: ‘template<template<class targetidentifierT> class ConnectionT> void nest::ModelManager::register_connection_model(const string&, nest::RegisterConnectionModelFlags)’ void register_connection_model( const std::string& name, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/nest/model_manager.h:197:8: note: template argument deduction/substitution failed: make[2]: *** [CMakeFiles/mymodule_module.dir/build.make:63: CMakeFiles/mymodule_module.dir/mymodule.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/mymodule_module.dir/all] Error 2 make: *** [Makefile:152: all] Error 2 ``` I am not sure how to deal with this, and any help would be appreciated. Thank you!

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Issue review VC Friday 10 Jan 10-13
by Hans Ekkehard Plesser 09 Jan '20

09 Jan '20

Dear all! We are going to have a NEST issue review VC tomorrow morning (Friday 10 Jan 10-13 CET) in the usual VC room for developer VCs (https://github.com/nest/nest-simulator/wiki/Connection-Details). The main aim is to review open issues in preparation of the NEST 3 merge and (eventually) release. Excuse the short notice, still booting up for 2020. Best, Hans Ekkehard -- 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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Open NEST Developer Video Conference Monday 6 January 2020 11:30 CET (UTC+1)
by Dennis Terhorst 05 Jan '20

05 Jan '20

Dear NEST Users & Developers! Happy new year 2020! I would like to invite you to this years first Open NEST Developer Video Conference, tomorrow Monday 6 January, 11.30-12.30 CET (UTC+1). As usual the agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-01-06-Open-NEST-Developer-… For details how to log in see below. 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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NO open NEST Developer Video Conference on 23 December 2019
by Dennis Terhorst 23 Dec '19

23 Dec '19

Dear NEST Developers! Best of seasons greetings to everyone! Since many people will not be available today we will skip the video conference. Our next regular meeting will be on January 6th. Merry Christmas to everyone! Enjoy the last days of 2019 and have a nice new-years! Looking forward to seeing all of you again in 2020! best, Dennis Terhorst https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Confe…

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NEST Conference 2020 — Save the Date: 29/30 June 2020 at Ås, Norway
by Hans Ekkehard Plesser 17 Dec '19

17 Dec '19

Dear NEST Users, We are happy to announce that the NEST Conference 2020 will again be held on NMBU's beautiful campus in Ås, Norway on 29 / 30 June 2020 followed by a NEST Hackathon until 3 July. More information will follow in a few weeks. Save the date & see you in the summer! Hans Ekkehard -- 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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Hackathon on CEREBELLUM MODELLING
by Dennis Terhorst 17 Dec '19

17 Dec '19

Dear simulation enthusiasts, The group in Pavia is preparing an event around CEREBELLUM MODELLING, in which you can see NEST and other simulators put to use on larger scale. It will be a nice occasion to meet with many other users, exchange experience and learn about model construction. Egidio, Claudia, Simona and team are organising this as a hackathon: Hackathon on CEREBELLUM MODELLING 13-15 January 2020, in Pavia. If you are interested in joining, please drop Simona Tritto an email:simona.tritto@unipv.it<mailto:simona.tritto@unipv.it> You can find the program attached. best, Dennis -- Dipl.-Phys. Dennis Terhorst Coordinator Software Development Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Theoretical Neuroscience, Institute for Advanced Simulation (IAS-6) Jülich Research Centre, Member of the Helmholz Association and JARA 52425 Jülich, Germany Building 15.22 Room 4004 Phone +49 2461 61-85062 Fax +49 2461 61- 9460 d.terhorst(a)fz-juelich.de

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Reset Network with to_file
by Maryada Maryada 08 Dec '19

08 Dec '19

Hi all, I am currently using nest.ResetNetwork() with to_file option and when I reset the network, seemingly it also deletes everything recorded so far by connected probes (spike detector, for instance). Any suggestions on how to avoid the deletion of previously written data on files. -- Thanks and Regards *Maryada*

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NEST 3 merge outlook
by Itaru Kitayama 06 Dec '19

06 Dec '19

Can somebody comment on this plan? I’m using the nest-3 branch heavily on FUGAKU and am wondering when it’ll be merged in the master.

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