Dear Nikolas,
Could the following example in NEST Simulator be what you're looking for?
https://github.com/nest/nest-simulator/blob/f28b138f469354264f65c3b5c9d05e5…
"""Check STDP protocol between two parrot_neurons connected by a stdp_synapse. Exact pre- and post-synaptic spike times are set by spike_generators connected to each parrot neuron. Additional spikes sent through the stdp_synapse are explicitly ignored in the postsynaptic parrot_neuron by setting the stdp_synapse to connect to port 1. """
With kind regards,
Charl
On Wed, Oct 30, 2019, at 11:58, Nikolaos Chrysanthidis wrote:
> Hi Charl,
> I want to test the weight change of a single synapse providing stimulation at 2 parrot neurons, so for that reason,
> If I excite two pre-,post- parrot neurons (parrot_A,B) using port 0, then the parrot_A will excite the parrot_B as well, so the parrot_B will end up having more spikes than expected.
> I think this can be overcome by using port1 of parrot_B in order to ignore the extra excitation from parrot_A.
> Please, I'd be grateful if you could provide a way to avoid extra excitation from parrot_A onto parrot_B.
>
> Kind regards,
> Nikolas
>
> *From:* Charl Linssen <nest-users(a)turingbirds.com>
> *Sent:* 28 October 2019 12:11
> *To:* users(a)nest-simulator.org
> *Subject:* [NEST Users] Re: parrot neurons PORT 1
>
> Dear Nikolaos,
>
> I'm a little confused as to why you wish to use port 1 for this. A synapse is not aware of incoming or outgoing ports, so if you want to test a particular synapse model, you can connect it between port 0 of a presynaptic parrot neuron, and port 0 of a postsynaptic parrot neuron. Could you otherwise please clarify your use case a bit?
>
> With kind regards,
> Charl
>
>
> On Thu, Oct 17, 2019, at 17:00, Nikolaos Chrysanthidis wrote:
>> Hi NEST users,
>>
>> I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development.
>>
>> To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor.
>> By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor.
>>
>> At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron
>> which I hope it will solve the error with the receptor.
>>
>> From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming
>> through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting
>>
>> two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron."
>>
>> My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ?
>> If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ?
>>
>> Thank you very much,
>> Kind regards,
>> Nikolas
>>
>>
>>
>>
>> _______________________________________________
>> NEST Users mailing list -- users(a)nest-simulator.org
>> To unsubscribe send an email to users-leave(a)nest-simulator.org
>>
>
Hi,
I'm trying to port to NEST this "conductance-based" network from Brian:
https://brian2.readthedocs.io/en/stable/examples/frompapers.Stimberg_et_al_…
I'm unable to reproduce their results (qualitatively - I'm not expecting
identical results since I assume RNGs, solvers and other implementation
details differ in many ways). Is there any publicly available example of a
random balanced network with conductance based synapses? From what I've
seen, all the brunel-style example networks are current based (as in the
original paper).
Thanks in advance,
Adam
Hi NEST users,
I have a pre- and post-synaptic spike train and I want to impose these spike trains onto a plastic synapse to see the weight development.
To this end, I thought of having 2 "parrot_neuron_ps" as pre- and post-synaptic neurons connected with the plastic synapse which uses AMPA receptor.
By doing this, NEST yields the following error: "NESTError: UnknownReceptorType in Connect_g_g_D_D: Receptor type 1 is not available in parrot_neuron_ps." which in my case Receptor type 1 is the AMPA receptor.
At the nest documentation about "parrot_neuron_ps" I found out that I can have the plastic synapse onto port 1 of the postsynaptic parrot neuron
which I hope it will solve the error with the receptor.
From nest documentation -> "Only spikes arriving on connections to port 0 will be repeated. Connections onto port 1 will be accepted, but spikes incoming
through port 1 will be ignored. This allows setting exact pre- and post-synaptic spike times for STDP protocols by connecting
two parrot neurons spiking at desired times by, e.g., a stdp_synapse onto port 1 on the post-synaptic parrot neuron."
My query is, how to connect the 2 neurons using port 1 of the post synaptic neuron ?
If this approach with parrot neurons doesn't seem the right choice, what is the most commonly used approach ?
Thank you very much,
Kind regards,
Nikolas
Dear NEST Developers!
I would like to invite you to our next bi-weekly Open NEST Developer
Video Conference today (please excuse the late invitation)
Monday 28 October, 11.30-12.30 CET (UTC+1).
See below for information about how to log into the meeting.
The agenda for this meeting is also available online, see
https://github.com/nest/nest-simulator/wiki/2019-10-14-Open-NEST-Developer-…
Agenda
1. Welcome
2. Planning of HBP High-Level Support Event in Heidelberg
<https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…>
next month
3. Review of NEST User Mailing List
<https://www.nest-simulator.org/mailinglist/hyperkitty/list/users@nest-simul…>
4. Review of open Github Pull Request
<https://github.com/nest/nest-simulator/pulls>
5. Review of open Github Issues
<https://github.com/nest/nest-simulator/issues>
Looking forward to seeing you soon!
best,
Dennis Terhorst
------------------
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Hi there,
I am trying to install nest under OSX Mojave and run into the following cmake-error (see below for a full trace):
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
I already tried various tricks (http://stechschulte.net/2016/03/20/openmp-osx-cmake.html, https://stackoverflow.com/questions/48825416/missing-openmp-c-flags-openmp-…), but had no success. Does anybody have experience?
Thanks in advance,
Benjamin
#########################################################
-- The CXX compiler identification is AppleClang 9.0.0.9000038
-- The C compiler identification is AppleClang 9.0.0.9000038
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Looking for include file inttypes.h
-- Looking for include file inttypes.h - found
-- Looking for include file mach-o/dyld.h
-- Looking for include file mach-o/dyld.h - found
-- Looking for include file mach/mach.h
-- Looking for include file mach/mach.h - found
-- Looking for include file memory.h
-- Looking for include file memory.h - found
-- Looking for include file stdint.h
-- Looking for include file stdint.h - found
-- Looking for include file sys/types.h
-- Looking for include file sys/types.h - found
-- Looking for C++ include istream
-- Looking for C++ include istream - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of long long
-- Check size of long long - done
-- Check size of u_int16_t
-- Check size of u_int16_t - done
-- Check size of uint16_t
-- Check size of uint16_t - done
-- Check size of u_int64_t
-- Check size of u_int64_t - done
-- Check size of uint64_t
-- Check size of uint64_t - done
-- Looking for NAN
-- Looking for NAN - found
-- Looking for isnan
-- Looking for isnan - found
-- Looking for M_E
-- Looking for M_E - found
-- Looking for M_PI
-- Looking for M_PI - found
-- Looking for expm1
-- Looking for expm1 - found
-- Host triple: x86_64-apple-darwin
-- Target triple: x86_64-apple-darwin
-- Found LTDL: /usr/local/lib/libltdl.dylib (found version "2.4.6")
-- Found Readline: /usr/lib/libreadline.dylib (found version "4.2")
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Found GSL: /usr/local/Cellar/gsl/2.6/include (found version "2.6")
-- Found PythonInterp: /Users/staude/.pyenv/shims/python (found version "3.7.2")
-- Found PythonLibs: /Users/staude/.pyenv/versions/3.7.2/lib/libpython3.7m.a (found suitable exact version "3.7.2")
-- Found Cython: /Users/staude/.pyenv/shims/cython (found version "0.29.13")
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
CMake Error at cmake/ProcessOptions.cmake:452 (message):
CMake can not find OpenMP.
Call Stack (most recent call first):
CMakeLists.txt:164 (nest_process_with_openmp)
Hello,
I would like to make a suggestion for future development. Now there is
a Python interface, but some of us have been working with C/C++ for
many years (and we have a lot of data processing software developed in
this language).
Please, could you include a C/C++ interface for NEST?
Thanks a lot in advance!
Xavier
Hi all,
I have a question regarding random number generator.
I am intend to randomly choose neuron population but keep this same across
multiple processes. (see attached)
mpirun -np 4 python network_population.py
However, seemingly I am missing something.
Also, in case I try to use different population count I am getting error
while connecting nodes with input or probes. (see mpi_example)
--
Thanks and Regards
*Maryada*
Dear NEST colleagues,
We like to inform you all about an event of the Human Brain Project,
that will take place in Heidelberg on November 25-28. It will be
comprised of introductory sessions on different types of infrastructure
that is being built for the neuroscience community. Among these will be
several NEST related sessions which may be of interest to you (see
attached file).
This is a combined event with a CodeJam and infrastructure trainings,
which will take place in close space-time proximity:
* 25 Nov: [Public event] EBRAINS - New enabling infrastructure for
neuroscience
* 26 Nov: How to increase the FAIRness of your research - an HBP
training course about data sharing
* *26-28 Nov: 2nd HPAC Platform Training *
* *26-28 Nov: CodeJam#10 *
The 2nd HPAC Platform Training will introduce the tools and services of
the High-Performance Analysis and Computing Platform and Fenix,
including an interactive session on how to apply for those resources.
There will also be several sessions about the simulators with different
resolutions being (co)developed in the HBP (Arbor, NEST and TVB).
More info and registration can be found here:
https://www.humanbrainproject.eu/en/education/participatecollaborate/infras…
The registration is already open but requires an account to register. If
you would like join the event please send an email to Maren Frings
<m.frings(a)fz-juelich.de> so we can create a guest account for you. Then
you can*register e.g. for the HPAC Training*. The events will have joint
breaks and it will be possible to switch to another event for the one or
the other session. You need to register only for the event you are most
interested in.
It would be great to see you there! :-)
Best regards,
Dennis & Maren
