11 Jun
2021
11 Jun
'21
1:19 p.m.
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I am
working on (It is a minor alteration: I included a minimum hard bound for
weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know what
is the best approach for doing this. Should I provide my copy of the
altered model file together with my project scripts? Or is there another
way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change
something on NEST code for a project.
Best,
Júlia
11 Jun
11 Jun
5:58 p.m.
_Hey Júlia!_
If its not of particular interest to all NEST users, but the readers of
your paper, I'd just put it up at ModelDB. They give you a permanent
link you can use for publication/reference, and just enough space for
additional scripts and documentation.
Kind regards,
\Florian
photo
*Florian Fiebig, PhD*
Researcher
Computational Brain Science
+46 70-744-7439 <tel:+16505426046> | Skype: florianfiebig <#>
<http://www.numenta.com/>
<http://us.linkedin.com/in/florian-fiebig-b387b886> Most recent
papers:<https://rdcu.be/bRLmu>
<https://doi.org/10.1523/JNEUROSCI.1989-16.2016>
<https://rdcu.be/bRLmu>
<https://www.eneuro.org/content/early/2020/02/28/ENEURO.0374-19.2020>
On 11/06/2021 13:19, Julia Gallinaro wrote:
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project
I am working on (It is a minor alteration: I included a minimum hard
bound for weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know
what is the best approach for doing this. Should I provide my copy of
the altered model file together with my project scripts? Or is there
another way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I
change something on NEST code for a project.
Best,
Júlia
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
14 Jun
14 Jun
1:21 p.m.
Dear Júlia,
do I understand you correctly that your change is really just the addition of some w_min
property, get/set_status() handling of it and some conditional code in the weight update
function? And am I right in that the behavior of the model currently in NEST would not be
changed at all if the new property were set to -infinity by default?
If the answers to these questions are close to “yes”, I think the best way to integrate
your changes into the corresponding built-in modes would be by means of a pull
request<https://nest-simulator.readthedocs.io/en/v3.0/contribute/development_workflow.html>
against NEST and/or NESTML.
If they are more towards “no” or “maybe”, I suggest, you come to one of our next open NEST
video
conferences<https://github.com/nest/nest-simulator/wiki/Open-NEST-Develo…ce>,
so we could discuss more directly.
Cheers,
Jochen!
On 11.06.21 13:19, Julia Gallinaro wrote:
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I am working on (It
is a minor alteration: I included a minimum hard bound for weights in the triplet STDP
rule).
I now want to share the code for this project, and would like to know what is the best
approach for doing this. Should I provide my copy of the altered model file together with
my project scripts? Or is there another way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change something on
NEST code for a project.
Best,
Júlia
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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,
Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
2:49 p.m.
Thanks, Florian! Thanks, Jochen!
@Jochen, the answer is mostly "yes" to both your questions. The only thing
is that there is already a conditional code in the weight update that sets
a minimum value of zero for the weight. I only changed the hardcoded zero
to a variable Wmin that can be set with set_status(). So the default value
of the property that would lead to no changes in the model behavior in NEST
is zero, and not -infinity. But I guess that still counts as a "yes".
I will look into a pull request, then. Thanks!
Cheers,
Júlia
Em seg., 14 de jun. de 2021 às 12:21, Jochen Martin Eppler <
j.eppler(a)fz-juelich.de> escreveu:
Dear Júlia,
do I understand you correctly that your change is really just the addition
of some w_min property, get/set_status() handling of it and some
conditional code in the weight update function? And am I right in that the
behavior of the model currently in NEST would not be changed at all if the
new property were set to *-infinity* by default?
If the answers to these questions are close to “yes”, I think the best way
to integrate your changes into the corresponding built-in modes would be by
means of a pull request
<https://nest-simulator.readthedocs.io/en/v3.0/contribute/development_workflow.html>
against NEST and/or NESTML.
If they are more towards “no” or “maybe”, I suggest, you come to one of
our next open NEST video conferences
<https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Conference>,
so we could discuss more directly.
Cheers,
Jochen!
On 11.06.21 13:19, Julia Gallinaro wrote:
Dear NEST Community,
I have performed a small alteration on one model of NEST for a project I
am working on (It is a minor alteration: I included a minimum hard bound
for weights in the triplet STDP rule).
I now want to share the code for this project, and would like to know what
is the best approach for doing this. Should I provide my copy of the
altered model file together with my project scripts? Or is there another
way of doing it, which is more appropriate?
I am sorry if that is a basic question, but it is the first time I change
something on NEST code for a project.
Best,
Júlia
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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,
Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
3:19 p.m.
Hi,
I agree with everything Jochen said. The NESTML synapse examples (see, for example, here
https://github.com/nest/nestml/pull/655/files#diff-b6340c6dd86cab42c436502a…)
already have a Wmin parameter, so don't need to be adapted. Code generation for the
triplet STDP plasticity rule still needs to be improved to account for that edge case we
talked about earlier on the list, however: https://github.com/nest/nestml/issues/661 /
https://github.com/nest/nest-simulator/issues/1990. Please stay tuned!
Kind regards,
Charl
On Mon, Jun 14, 2021, at 14:49, Julia Gallinaro wrote:
Thanks, Florian! Thanks, Jochen!
@Jochen, the answer is mostly "yes" to both your questions. The only thing is
that there is already a conditional code in the weight update that sets a minimum value of
zero for the weight. I only changed the hardcoded zero to a variable Wmin that can be set
with set_status(). So the default value of the property that would lead to no changes in
the model behavior in NEST is zero, and not -infinity. But I guess that still counts as a
"yes".
I will look into a pull request, then. Thanks!
Cheers,
Júlia
Em seg., 14 de jun. de 2021 às 12:21, Jochen Martin Eppler <j.eppler(a)fz-juelich.de>
escreveu:
> Dear Júlia,
> do I understand you correctly that your change is
really just the addition of some ` w_min` property, get/set_status() handling of it and
some conditional code in the weight update function? And am I right in that the behavior
of the model currently in NEST would not be changed at all if the new property were set to
*-infinity* by default?
> If the answers to these questions are close to
“yes”, I think the best way to integrate your changes into the corresponding built-in
modes would be by means of a pull request
<https://nest-simulator.readthedocs.io/en/v3.0/contribute/development_workflow.html>
against NEST and/or NESTML.
> If they are more towards “no” or “maybe”, I
suggest, you come to one of our next open NEST video conferences
<https://github.com/nest/nest-simulator/wiki/Open-NEST-Developer-Video-Conference>,
so we could discuss more directly.
>
>> Cheers,
>> Jochen!
>
> On 11.06.21 13:19, Julia Gallinaro wrote:
>
>
>>> Dear NEST Community,
> >
>>> I have performed a small
alteration on one model of NEST for a project I am working on (It is a minor alteration: I
included a minimum hard bound for weights in the triplet STDP rule).
> >
>>> I now want to share the code
for this project, and would like to know what is the best approach for doing this. Should
I provide my copy of the altered model file together with my project scripts? Or is there
another way of doing it, which is more appropriate?
> >
>>> I am sorry if that is a basic
question, but it is the first time I change something on NEST code for a project.
> >
>>> Best,
>>> Júlia
> >
>>>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
> >
>
>
>
>> --
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
>
>
>>
------------------------------------------------------------------------------------------------
>>
------------------------------------------------------------------------------------------------
>> 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,
>> Dr. Astrid Lambrecht, Prof. Dr. Frauke Melchior
>>
------------------------------------------------------------------------------------------------
>>
------------------------------------------------------------------------------------------------
>> _______________________________________________
>> NEST Users mailing list -- users(a)nest-simulator.org
>> To unsubscribe send an email to users-leave(a)nest-simulator.org
> _______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
<mailto:users%40nest-simulator.org>
> To unsubscribe send an email to users-leave(a)nest-simulator.org
<mailto:users-leave%40nest-simulator.org>
>
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4 comments
4 participants
participants (4)
-
Charl Linssen -
Florian Fiebig -
Jochen Martin Eppler -
Julia Gallinaro