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Please merge master if you have open pull requests / Issue #1449
by Hans Ekkehard Plesser 12 Mar '20

12 Mar '20

Dear NEST Developers! If you currently have an open pull request against the NEST master branch on Github, please merge the most recent updates from master into your branch. A bug described in #1449 and fixed by #1458 lead to non-deterministic test suite failures. Once you have merged master into your branch, please push again to Github to re-run the tests on Travis. 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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A question about NESTML: parameters inherited from Archiving Node aren't exposed to Get/SetStatus
by Alexey Serenko 06 Mar '20

06 Mar '20

Dear community, Sorry if this is off-topic for this list, but I am facing a problem with NESTML. After compiling any of the example neuron models present in the repository, the model seems not to have parameters inherited from ArchivingNode (such as, for instance, an STDP parameter tau_minus) available for GetStatus() or SetStatus(). Oddly enough, the model probably does possess these parameters, because can be connected to/from TDP synapses, but just does not expose them to Get/SetStatus. Could you please advise what I should do to examine the problem? I am using NEST version 2.20 and NESTML version 3.0.post0.dev5 (pip-installed). Faithfully yours, Alex Serenko, graduate student at Kurchatov Institute, Moscow, Russia

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nest3: How to create composite of SynapseCollections
by benedikt.s.vogler＠tum.de 03 Mar '20

03 Mar '20

Hello everyone! I am transitioning my Code from nest 2 to nest 3. In nest 2 I used a list of connections and could use this list with nest.Get/SetStatus(). With nest 3 I now have a list of SynapseCollections instances, where each synapse collection contains only one connection. For node collections, there seems to be an operator to create a composite (https://nest-simulator.readthedocs.io/en/latest/guides/from_nest2_to_nest3.…). For SynapseCollections, however, I was unable to use the plus operator and could not find similar documentation as in the transition guide. My current workaround is to loop over each instance the list and call Set() on each instance/synapse. What is the recommended way to create a SynapseCollections from many? Is there somewhere more documentation covering nest 3 than the two pages covering the changes form nest 2 to 3? Kind regards, Benedikt S. Vogler

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Open NEST Developer Video Conference Monday 2 March 2020 11:30 CET (UTC+1)
by Dennis Terhorst 02 Mar '20

02 Mar '20

Dear NEST Users & Developers! I would like to invite you to our next bi-weekly Open NEST Developer Video Conference, today Monday 2 March, 11.30-12.30 CET (UTC+1). In today's meeting we will focus on the development status of some critical pull-requests/issues. Agenda Welcome Review of NEST User Mailing List Critical issues Issue #1394, PR #1442 Issue #1409, PR #1409 Issue #1449 Random numbers in NEST3 see Issue #1440 Review of open Github Pull Request Review of open Github Issues If you feel uncomfortable to join meetings in larger groups, consider to dial in via video from your desk (details how to log in are given below, as usual). The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2020-03-02-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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Install nest-simulator-2.20.0 failed in Ubuntu 14.04
by 1033471810＠qq.com 01 Mar '20

01 Mar '20

Hello everyone, I followed the instructions to install nest-simulator-2.20.0 in my Ubuntu. When I do the things follow: ------------------------------------------------------------------------------- cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr/bin/nest /home/visapy_and_dependencies/nest-simulator-2.20.0 make make install -------------------------------------------------------------------------------- Unfortunately, during "make" it reports some Error, see following: [ 49%] Building CXX object nestkernel/CMakeFiles/nestkernel.dir/connection_manage.cpp.o /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managercpp:419:1: error: prototype for ‘void nest::ConnectionManager::connect(nest::inde, nest::Node*, nest::thread, nest::synindex, const DictionaryDatum&, double, doube)’ does not match any in class ‘nest::ConnectionManager’ nest::ConnectionManager::connect( const index sgid, ^~~~ In file included from /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkerel/connection_manager.cpp:23:0: /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managerh:135:8: error: candidates are: bool nest::ConnectionManager::connect(nest::inde nest::index, const DictionaryDatum&, nest::synindex) bool connect( const index sgid, const index target, const DictionaryDatum& parms, const synindex syn_id ); ^~~~~~~ /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managerh:117:8: error: void nest::ConnectionManager::connect(nest::index nest::Node*, nest::thread, nest::synindex, const DictionaryDatum&, double_t, doule_t) void connect( const index sgid, ^~~~~~~ /home/visapy_and_dependencies/nest-simulator-2.20.0/nestkernel/connection_managercpp:352:1: error: void nest::ConnectionManager::connect(const nes::GIDCollection&, const nest::GIDCollection&, const DictionaryDatum&, const DictinaryDatum&) nest::ConnectionManager::connect( const GIDCollection& sources, ^~~~ make[2]: *** [nestkernel/CMakeFiles/nestkernel.dir/connection_manager.cpp.o] Erro 1 make[1]: *** [nestkernel/CMakeFiles/nestkernel.dir/all] Error 2 make: *** [all] Error 2 I have no idea about this, I'd appreciate it if you could help me. and my cmake version 3.10.1, gcc version 7.4.0

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warning: 'GetConnections' are now invalid
by Lea Steffen 28 Feb '20

28 Feb '20

Hi everybody, I switched from Nest 2.16 to 2.20 and now I get this warning message: ConnectionManager [Warning]: New connections created, connection descriptors previously obtained using 'GetConnections' are now invalid This happens at several parts in my code while building synapses with 'sim.Projection(...)'. I use a 'FromListConnector' and 'STDPMechanism' as synapse_type. I neversaw this warning in the previous Nest version, is it something to be concerned about? I am not quite sure what it is trying to tell me. Thanks in advance, Lea ......................................................... M. Sc. Lea Steffen Wissenschaftlicher Mitarbeiter | Research Scientist Intelligent Systems and Production Engineering (ISPE) Interactive Diagnosis and Service Systems (IDS) FZI Forschungszentrum Informatik Haid-und-Neu-Str. 10–14 76131 Karlsruhe, Germany Tel.: +49 721 9654-218 steffen(a)fzi.de www.fzi.de/mitarbeiter/steffen ......................................................... FZI Forschungszentrum Informatik am Karlsruher Institut für Technologie Stiftung des bürgerlichen Rechts Stiftung Az: 14-0563.1 Regierungspräsidium Karlsruhe Vorstand: Prof. Dr. Andreas Oberweis, Jan Wiesenberger, Prof. Dr.-Ing. J. Marius Zöllner Vorsitzender des Kuratoriums: Ministerialdirigent Günther Leßnerkraus .........................................................

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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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