I'm trying to install and use NEST on google Colab, but it's not importing:
!pip install -Uqq nest
!pip install -Uqq nestml
!pip install -Uqq pysilsub
import nest
import nestml
import numpy as np
import matplotlib.pyplot as plt
from pysilsub import observers
from nestml.network import Network
from nestml.models import ConeNakaRushton
Am I able to use NEST on Google Colab?
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
Dear all,
I am trying to develop a new synapse model that uses the activity of the postsynaptic neuron. I'm looking at the STDP synapse to understand how it gets the target neuron history, and I wanted to clarify: are t_spike and t_lastspike the time stamps for the last spike of the presynaptic or postsynaptic neuron? I am looking at the send method of stdp_synapse.h (https://github.com/nest/nest-simulator/blob/91a02ed98017224deabe25e8e08bcfd…)
Thanks in advance!
Best,
Priyanka Rao
Hi,
We recently discovered that multimeter returns membrane potential in some unordered way so if we want to record the last state of a group of neurons and then to continue simulation from exactly the same state we were unable to reconstruct it properly.
Is there a way to record the membrane potential together with neuron ID?
Best,Petia Koprinkova-Hristova
Dear NEST Users & Developers,
we're currently working on a custom OpenMPI BTL (supporting a custom
FPGA-based NIC) at the National Institute for Nuclear Physics in Rome,
Italy and we have an error when running hpc_benchmark(this test is
currently used as simple validation test) with 2 processes (one on each
of 2 hosts), the command we run is like:
mpirun -n 2 -H host1:1,host2:1 --bynode --report-bindings -mca btl
apelink,self,sm python hpc_benchmark.py (apelink is our custom BTL
component)
but then we see this error:
python:
[...]/NEST_with_local_ompi/nest-simulator-3.6/nestkernel/target_table.cpp:107:
void nest::TargetTable::add_target(size_t, size_t, const
nest::TargetData&): Assertion `syn_id < secondary_send_buffer_pos_[ tid
][ lid ].size()' failed. [host:23979] *** Process received signal ***
[host:23979] Signal: Aborted (6) [host:23979] Signal code: (-6)
My guess is that we are transferring something incorrectly (maybe during
the initialization/setup phase?), but I'm not sure what the assert
expects to have in secondary_send_buffer_pos_[ tid ][ lid ].size() and
how this field should be set.
Best,
Michele
Dear NEST Users & Developers!
I would like to invite you to our next fortnightly Open NEST Developer Video Conference today
*Monday January 29, at 11:30 CET (UTC+0100).*
As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams.
The remainder of the meeting we would go into a bunch of topics that came up and that were suggested by the teams.
Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section.
Agenda
* Welcome
* Review of NEST User Mailing List
* Project team round
* In-depth discussion
o Changed Model registration for NEST Models (from last meeting)
o Proposed new model with an approximation for nonlinear NMDA receptors (#2979 <https://github.com/nest/nest-simulator/pull/2979>)
o Proposed multi-state models (#3069 <https://github.com/nest/nest-simulator/pull/3069>)
o Report from LASCON IX
The agenda for this meeting is also available online, see https://github.com/nest/nest-simulator/wiki/2024-01-29-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-01-29-Open-NEST-Developer-…>
Looking forward to seeing you soon!
Cheers,
Dennis Terhorst
Log-in information
We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4>
--
Dipl.-Phys. Dennis Terhorst
Coordinator Software Development
Institute for Advanced Simulation (IAS-6), Computational and Systems Neuroscience &
JARA-Institute Brain Structure-Function Relationships (INM-10)
Institute of Neuroscience and Medicine
Jülich Research Center, Member of the Helmholz Association
52425 Jülich, Germany
http://www.csn.fz-juelich.de/
Phone +49 2461 61-85062
----------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
----------------------------------------------------------------------
I'm using Google Bard's Gemini to learn NESTML. It's giving me some
unexpected results:
import nestml
from nestml.network import Network
from nestml.models import ConeNakaRushton
# Define network with Naka-Rushton cone model for primate 'cone_type' cones
network = Network()
cone_population = network.add_population("cones", ConeNakaRushton(species=
"human", cone_type=cone_type))
The NESTML network and models packages don't seem to exist. Also, how do I
find more information about the network and models packages (or packages in
general) for NESTML?
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
Dear NEST Users & Developers!
🎈🎉🎈 Happy New Year! 🎈🎊🎈
I would like to invite you to our first fortnightly Open NEST Developer Video Conference in 2024, today
*Monday January 15, at 11:30 CET (UTC+0100).*
As usual, in the Project team round, a contact person of each team will give a short statement summarizing ongoing and planned work in the team and highlight cross-cutting points that need discussion among the teams. The remainder of the meeting we would go into a more in-depth discussion of topics that came up on the mailing list or that are suggested by the teams.
Feel free to join the meeting also if it’s just to bring your own quick questions for direct discussion in the in-depth section.
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/2024-01-15-Open-NEST-Developer-… <https://github.com/nest/nest-simulator/wiki/2024-01-15-Open-NEST-Developer-…>
Looking forward to seeing you soon!
Cheers,
Dennis Terhorst
Log-in information
We use a virtual conference room provided by DFN <https://www.dfn.de/en/> (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 <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 <mailto: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 <http://vcc.zih.tu-dresden.de/index.php?linkid=1.1.3.4>
--
Dipl.-Phys. Dennis Terhorst
Coordinator Software Development
Institute of Neuroscience and Medicine
Computational and Systems Neuroscience (INM-6) &
Institute for Advanced Simulation (IAS-6)
Theoretical Neuroscience & JARA (INM-10)
Jülich Research Center, Member of the Helmholz Association
52425 Jülich, Germany
http://www.csn.fz-juelich.de/
Phone +49 2461 61-85062
----------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
----------------------------------------------------------------------
