29 Mar
2024
29 Mar
'24
1:32 a.m.
Thank you Hans,
I'd like to share the nest code I've created with teammates, and run the
code within our Google Colab code base. So, I've gotten nest and nestml to
import, but run an error whenever I try to call a submodule:
NEST:
#Instructions from:
##
https://nest-simulator.readthedocs.io/en/stable/installation/developer.html
!git clone https://github.com/nest/nest-simulator
import nest
import matplotlib.pyplot as plt
neuron = nest.Create("iaf_psc_alpha")
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-13-525a46cfa676>
<https://al313cotm5f-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab_20240228-060152_RC00_611016369#>
in <cell line: 6>() 4 import nest 5 import matplotlib.pyplot
as plt
----> 6 neuron = nest.Create("iaf_psc_alpha")
AttributeError: module 'nest' has no attribute 'Create'
NESTML:
#Instructions from:
##
https://nestml.readthedocs.io/en/latest/installation.html#installing-the-la…
!git clone https://github.com/nest/nestml
%cd nestml
!pwd
!python setup.py install
!pip install git+https://github.com/nest/ode-toolbox
!python setup.py test
!pip install -Uqq pysilsub
!pip install -Uqq nest
import sklearn
import scipy
import nest
import pynestml as nestml
import numpy as np
import matplotlib.pyplot as plt
from pysilsub import observers
nestml.help('Create')
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-14-9be5eaa06f5d>
<https://al313cotm5f-496ff2e9c6d22116-0-colab.googleusercontent.com/outputframe.html?vrz=colab_20240228-060152_RC00_611016369#>
in <cell line: 19>() 17 import matplotlib.pyplot as plt 18
from pysilsub import observers
---> 19 nestml.help('Create') 20
AttributeError: module 'pynestml' has no attribute 'help'
I appreciate any help to install and use the software,
On Thu, Jan 4, 2024 at 2:39 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
As an alternative, the EBRAINS research infrastructure offers
collaboratories with NEST and many other neuroscience tools pre-installed,
see
https://www.ebrains.eu/data/collaboratory
https://www.ebrains.eu/tools/nest
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
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
Home http://arken.nmbu.no/~plesser
*From: *Robin Gilbert De Schepper <robingilbert.deschepper(a)unipv.it>
*Date: *Thursday, 4 January 2024 at 10:44
*To: *NEST User Mailing List <users(a)nest-simulator.org>
*Subject: *[NEST Users] Re: NEST on Google Colab?
NEST is not pip installable, using !pip install -Uqq nest will install a
"network stack tester" https://pypi.org/project/nest/
You will have to follow another installation route. I'm not sure which one
is recommended for Google Collab. Perhaps the conda or CMake installation?
On Sat, 23 Dec 2023 at 00:58, Anthony Lee <anthonyylee(a)colorado.edu>
wrote:
Hey Alvin,
You may have to restart the kernel because the installation was installed
via a child shell process and have yet to be loaded into the current
process that the kernel is running on.
IIRC, it is called “Restart runtime” in Google Colab.
Anthony
On Dec 22, 2023, at 12:46, Alvin Spivey <alvin.spivey(a)gmail.com> wrote:
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
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To unsubscribe send an email to users-leave(a)nest-simulator.org
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Robin De Schepper, PhD (they/them)
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/
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055