May 2020 - NEST Users - NEST Initiative Mail

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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Error: UnknownModelName
by Allen Rabayda 27 Jun '20

27 Jun '20

Dear Nest Community, Would anyone have insight into why I'm getting an UnknownModelName error? I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS). Thanks for any help. Best Regards, --Allen **** Error Message--additional details attached ****** raise exceptionCls(commandname, message) nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D: /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.', 'UnknownModelName', <SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict for a list of available models.') ********************************************************

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pipnest
by Robin Gilbert De Schepper 17 Jun '20

17 Jun '20

Hi, I created a little tool that provides packaging for NEST extension modules into python packages that can be `pip installed` on the target machine. https://pip-nest.readthedocs.io/en/latest/ First off, is this interesting to the community? It certainly seems easier to `pip install some-module` than to provide installation instructions, and I can now specify my modules as dependencies in code I distribute. Secondly, there are some shortcomings based on the fact that the pip install only reliably produces the build artifacts into python's site-packages and nest doesn't look for them there. This can probably only be elegantly solved by adding an `entry_point` to the nest python module so that these pip nest modules can announce themselves there? -- Robin De Schepper, MSc Department of Brain and Behavioral Sciences Unit of Neurophysiology University of Pavia, Italy Via Forlanini 6, 27100 Pavia - Italy Tel: (+39) 038298-7607 http://www-5.unipv.it/dangelo/

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send() function
by Itaru Kitayama 01 Jun '20

01 Jun '20

Hi, How do I check where send() function implemented in connector_base.h is generated and stored in which object file? Itaru.

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NEST Conference website not reachable
by Bruno Golosio 30 May '20

30 May '20

Hello, the deadline for submission of contributions is approaching and the NEST Conference website is down since yesterday. Is there an alternative way to submit contributions? Bruno -- Bruno Golosio, PhD Associate Professor of Applied Physics Coordinator of the School of Medical Physics Department of Physics University of Cagliari (Italy) [image: image.gif]

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Finding the right parameters for the balanced network
by nosratullah mohammadi 26 May '20

26 May '20

Dear Nest Users, I hope all of you be in health during these times. I want to create a balanced network as it’s the first step of my master thesis. The model I want to use is “iaf_cond_exp” which is a must for later purposes. There’s an example in Pynest folder of a balanced network, unless it’s using “iaf_psc_alpha” and it doesn’t fit my goals. When I try to change the model, and run the program, the network doesn’t get active and there’s nothing to record. I divided my question into two part: - Does anyone have a balanced network with “iaf_cond_exp” neurons and all of its necessary parameters to run? - In general, how do people find or calculate their network parameters to fit the neuron model they use and don’t get lost in the massive number of parameters. Note: I also tried to use the example of “brunel_alpha_evolution_strategies.py” example which is a genetic algorithm to find the best parameter, although it finds the parameters after 50 generation, I use those parameters afterwards. It just doesn’t work! Kind regards, Nosratullah Mohammadi

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NEST Conference 2020 — Submission deadline 1 June 2020
by Anne Elfgen 26 May '20

26 May '20

Dear all, Just a little reminder that the submission deadline for the (virtual) NEST Conference 2020 is *this Monday, June 1st. *We are looking forward to your contributions. The NEST Conference provides an opportunity for the NEST Community to meet, exchange success stories, swap advice, learn about current developments in and around NEST spiking network simulation and its application. This year's conference will take place as a *virtual conference* on *Monday/Tuesday 29/30 June 2020*. We are inviting contributions to the conference, including plenary talks, "posters" and breakout sessions on specific topics. *Important dates* *01 June 2020* — Deadline for submission of contributions *08 June 2020* — Notification of acceptance *10 June 2020* — Deadline for NEST Initiative Membership applications (registration is free for members in 2020) *22 June 2020* — Registration deadline *29 June 2020* — NEST Conference 2020 starts For more information on how to submit your contribution, register and participate, please visit the conference website *https://nest-simulator.org/conference* We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Susanne Kunkel, Dennis Terhorst, Anne Elfgen & many more

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Open NEST Developer Video Conference Monday 25 May 2020 11:30 CEST (UTC+2)
by Dennis Terhorst 25 May '20

25 May '20

Dear NEST Users & Developers! I would like to invite you to our next fortnightly Open NEST Developer Video Conference on Monday 25 May, 11.30-12.30 CEST (UTC+2). 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 suggested from 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/2020-05-25-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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Reset Kernel + STDP Performance
by Benedikt S. Vogler 22 May '20

22 May '20

Hello everyone! I am writing to you regarding two matters: Reset Network/Kernel in nest2->nest 3 In the last developer conference, Daphne Cornelisse talked about that she used ResetNetwork() to solve her problem. ResetNetwork() is marked as deprecated. No one said anything, so I got confused why this is apparently the recommended way or at least approved. She showed me, that it works (in her case). It is deprecated, so there is probably some good reasoning behind it. The documentation says: "ResetNetwork is deprecated and will be removed in NEST 3, because this function is not fully able to reset network and simulator state. What are the edge cases where the use causes problems? In this ticket, it is stated that the feature is just removed with any replacement. https://github.com/nest/nest-simulator/issues/525 Thus, in nest3 there is only ResetKernel(). This means that you have to rebuild the network for any application where you do multiple simulations with different input or parameter changes. I am using nest3 for reinforcement learning and in each training episode, I have to extract all the weights and save them, reset the kernel, reconstruct the net, then load all the weights. This adds a lot of overhead in performance and bloats my code. I basically have another front-end storing the net and talking to the nest back-end. Therefore, the update to nest3 is a downgrade for many applications. I don’t have a solution for this issue, but I want to spark some discussion as I learned that I am not the only nest user to stumble into this issue. STDP Performance boost by manual computation in python In the paper "Demonstrating Advantages of Neuromorphic Computation: A Pilot Study“ by Wunderlich et al. (https://www.frontiersin.org/articles/10.3389/fnins.2019.00260/full) some performance improvement on STDP was reported. "The synaptic weight updates in each iteration were restricted to those synapses which transmitted spikes, i.e., the synapses from the active input unit to all output units (32 out of the 1,024 synapses), as the correlation a+ of all other synapses is zero in a perfect simulation without fixed-pattern noise. This has the effect of reducing the overall time required to simulate one iteration[…]“ The provided source code (https://github.com/electronicvisions/model-sw-pong/blob/976e0778ca05cfd96c4… <https://github.com/electronicvisions/model-sw-pong/blob/976e0778ca05cfd96c4…>) indeed contains a manual computation of STDP. When using the nest library I don’t expect to do some computation in python to be faster. It appears to me that the nest implementation is computing STDP every time, even without spikes? Maybe someone can comment on this whether this can be improved in nest? Kind regards, Benedikt S. Vogler -- Benedikt S. Vogler benedikt.s.vogler(a)tum.de Student M.Sc. Robotics, Cognition, Intelligence

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Inhibitory plasticity with current based neurons
by Julia Gallinaro 11 May '20

11 May '20

Dear all, I would like to simulate a network of current based LIF ('iaf_psc_delta') with inhibitory plasticity. I tried using the model vogels_sprekeler_synapse, but the resulting weights are positive (and they increase when firing rate is high). I guess it is because when used with conductance based neurons, the resulting weights would be multiplied by a gI<0? And with current based neurons, this is not the case. The weight is directly used as the synaptic weight. Do I understand it right? Is there a way to implement inhibitory plasticity using the vogels_sprekeler_synapse and current based LIF? Best, Júlia

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NEST Users May 2020