- NEST Users - NEST Initiative Mail

Iaf - psc - delta neurons data
by Parva Alavian 16 Apr '21

16 Apr '21

Dear developers/users of nest, I am using the iaf-psc-delta neurons in my network and I need to access the information on the amount of excitatory and inhibitory input that each neuron is receiving in time in order to study balance.(so not just I-e but also the inputs that it is getting from other neurons in the randomly connected network). Can you please help me with this? It would also help if I knew where to find the indices of all the neurons that are presynaptic to a given neuron (a connectivity matrix). I would then be able to calculate the input current myself. Looking forward to hearing from you! Kind regards, Parva

1 0

Triplets STDP model
by Julia Gallinaro 14 Apr '21

14 Apr '21

Dear NEST community, I am working with the triplets STDP connection on NEST simulations, and I am interested in how the weight dynamics change when the spike trains are altered in some specific ways. In order to do that, I run a network simulation using NEST and the triplets STDP rule and save the full spike trains of two neurons which are synaptically connected (one pre and one post). I then recreate the weight changes on a code outside the NEST loop, so that I can manipulate the spike trains and observe what happens to the synaptic weights. Trying to validate this approach, though, I find that my code (outside NEST loop) generates different weight values than the NEST simulation when using the same spike trains generated during the simulation. I guess I have some error in my implementation of the triplets rule. I thought it could be something with the implementation of the delays, or the moment when the weights are measured in the simulation, but I have had no success trying to fix it yet. I know this is not exactly a NEST issue, but I thought I would give it a try and ask here at the list. In case someone has already worked with the triplets rule and could point me out to what is/could be wrong in my implementation, I would very much appreciate it :) Thanks! best, Júlia

3 7

CreateLayer problem with dictionary
by xotazu＠cvc.uab.es 13 Apr '21

13 Apr '21

Hello, I am having a basic problem creating layers with topology (pyhton 3.6 and NEST 2.20.1). It always complains about the dictionary sent to CreateLayer, telling it is a number. The code below correctly prints <class 'dict'> but prints this error: Traceback (most recent call last): File "test/binary_gdf.py", line 9, in <module> kk=tp.CreateLayer({'extent': [1, 1],'rows': 20, 'columns': 20,'elements' : 'izhikevich','edge_wrap':True}) File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/topology/hl_api.py", line 650, in CreateLayer return topology_func('{ CreateLayer } Map', specs) File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/topology/ll_api.py", line 61, in topology_func return nest.ll_api.sli_func(slifunc, *args) File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/ll_api.py", line 182, in sli_func sli_run(slifun) # SLI support code to execute s on args File "/home/neurobit/local/nest-py3/lib64/python3.6/site-packages/nest/ll_api.py", line 132, in catching_sli_run raise exceptionCls(commandname, message) nest.lib.hl_api_exceptions.TypeMismatch: ('TypeMismatch in CreateLayer_D: Expected datatype: doubletype\nProvided datatype: integertype', 'TypeMismatch', <SLILiteral: CreateLayer_D>, ': Expected datatype: doubletype\nProvided datatype: integertype') Any help would be nice :-) Xavier ---- import nest import nest.topology as tp nest.SetKernelStatus({"overwrite_files": True}) my_dict = {'extent': [1, 1],'rows': 20, 'columns': 20,'elements' : 'izhikevich','edge_wrap':True} print(type(my_dict)) kk=tp.CreateLayer(my_dict)

2 3

NEST Conference 2021 goes virtual — registration & call for contributions open
by Hans Ekkehard Plesser 13 Apr '21

13 Apr '21

Dear all, The NEST Initiative is excited to invite everyone interested in Neural Simulation Technology and the NEST Simulator to the NEST Conference 2021. 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 again take place as a virtual conference on Monday/Tuesday 28/29 June 2021 followed by a virtual NEST User Hackathon until Friday 2 July, which offers the opportunity to deep-dive your own code with expert developers at your fingertips. Registration and submission of contributions are now open! We are inviting contributions to the conference, including plenary talks, "posters", breakout sessions and workshops on specific topics. Please register and submit your contribution(s) via the conference website https://nest-simulator.org/conference. Important dates 16 May 2021 — Deadline for submission of contributions and for NEST Initiative Membership applications 08 June 2021 — Notification of acceptance 21 June 2021 — Registration deadline 28 June 2021 — NEST Conference 2021 starts We are looking forward to seeing you all in June! Hans Ekkehard Plesser, Dennis Terhorst & Anne Elfgen -- 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

1 0

Writing gdf files in binary format
by Xavier Otazu 13 Apr '21

13 Apr '21

Hello, I am trying to write spikedector data into .gdf files in binary format, but I cannot. I am setting the 'binary' param of the spikedetector to True (I checked it using nest.GetStatus) but files are written in ASCII. Do I need some special python package? I am using python 2.7.5 and NEST 2.18. Thanks in advance. Xavier Computer Vision Center<http://www.cvc.uab.cat> CONFIDENTIALITY WARNING<http://www.cvc.uab.es/?page_id=7475>

3 3

Data Science Morning Coffee
by Hans Ekkehard Plesser 12 Apr '21

12 Apr '21

Dear all! Here the morning coffees are back in Outlook. We meet at https://nmbu.zoom.us/j/940209461. Best, Hans Ekkehard

2 2

Canceled: Data Science Morning Coffee
by Hans Ekkehard Plesser 12 Apr '21

12 Apr '21

Dear all! Here the morning coffees are back in Outlook. We meet at https://nmbu.zoom.us/j/940209461. Best, Hans Ekkehard

1 0

Canceled: Data Science Morning Coffee
by Hans Ekkehard Plesser 12 Apr '21

12 Apr '21

Dear all! Here the morning coffees are back in Outlook. We meet at https://nmbu.zoom.us/j/940209461. Best, Hans Ekkehard

1 0

Re: Spatial grid + jitter
by Hans Ekkehard Plesser 07 Apr '21

07 Apr '21

Dear Jasper, In NEST 3, this should be possible. Stine or Håkon, could you provide some advice? 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 On 06/04/2021, 12:05, "Albers, Jasper" <j.albers(a)fz-juelich.de<mailto:j.albers@fz-juelich.de>> wrote: Dear all, a colleague of mine (in CC) and myself are implementing a spatially structured network in NEST (using current NEST master). We are wondering how to generate a population of neurons that are distributed on a regular grid plus a random jitter. This means that we want to end up with a spatial distribution as can be seen in Figure 8 in the tutorial for creating spatially structured networks<https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>. Below that figure one finds a code snippet; however, we believe that this does not correspond to the distribution of Figure 8. In the documentation of NEST 2.20.1 we did find a code snippet that produces a jittered grid: import numpy as np # grid with jitter jit = 0.03 xs = np.arange(-0.5,.501,0.1) poss = [[x,y] for y in xs for x in xs] poss = [[p[0]+np.random.uniform(-jit,jit),p[1]+np.random.uniform(-jit,jit)] for p in poss] layer_dict_ex = {"positions": poss, "extent" : [1.1,1.1], "elements" : "iaf_psc_alpha"} As is apparent, this code does not make use of NEST internal random number generation but rather produces a list of positions that is then passed to a layer. Thus our question is: is it possible to create a jittered grid natively in NEST master? Best regards, Jasper and Anno ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

2 1

Spatial grid + jitter
by Albers, Jasper 06 Apr '21

06 Apr '21

Dear all, a colleague of mine (in CC) and myself are implementing a spatially structured network in NEST (using current NEST master). We are wondering how to generate a population of neurons that are distributed on a regular grid plus a random jitter. This means that we want to end up with a spatial distribution as can be seen in Figure 8 in the tutorial for creating spatially structured networks<https://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/p…>. Below that figure one finds a code snippet; however, we believe that this does not correspond to the distribution of Figure 8. In the documentation of NEST 2.20.1 we did find a code snippet that produces a jittered grid: import numpy as np # grid with jitter jit = 0.03 xs = np.arange(-0.5,.501,0.1) poss = [[x,y] for y in xs for x in xs] poss = [[p[0]+np.random.uniform(-jit,jit),p[1]+np.random.uniform(-jit,jit)] for p in poss] layer_dict_ex = {"positions": poss, "extent" : [1.1,1.1], "elements" : "iaf_psc_alpha"} As is apparent, this code does not make use of NEST internal random number generation but rather produces a list of positions that is then passed to a layer. Thus our question is: is it possible to create a jittered grid natively in NEST master? Best regards, Jasper and Anno ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

1 0

2025

2024

2023

2022

2021

2020

2019

NEST Users