9 Apr
2024
9 Apr
'24
8:39 p.m.
Hi Alvin,
#Instructions from:
##https://nest-simulator.readthedocs.io/en/stable/installation/developer.html
!git clone https://github.com/nest/nest-simulator
If you clone NEST, you then need to compile it. On Google Colab, it you might want to try
to install NEST via Conda/Mamba.
import nest
import matplotlib.pyplot as plt
neuron = nest.Create("iaf_psc_alpha")
This likely did not import the NEST Simulator package nest but something else. When NEST
is imported, you will see a message like
In [1]: import nest
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version: 3.7.0-rc1
Built: Apr 5 2024 08:41:00
This program is provided AS IS and comes with
NO WARRANTY. See the file LICENSE for details.
Problems or suggestions?
Visit https://www.nest-simulator.org
Type 'nest.help()' to find out more about NEST.
---------------------------------------------------------------------------
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-latest-development-version-from-github
!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')
nestml does not have a help() function, but nest.help(‘Create’) should work (don’t cut and
paste that last piece of code, I could not stop Outlook from modifying the quotes).
Best regards,
Hans Ekkehard
---------------------------------------------------------------------------
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@nmbu.no<mailto:hans.ekkehard.plesser@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@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>
Home http://arken.nmbu.no/~plesser
From: Robin Gilbert De Schepper
<robingilbert.deschepper@unipv.it<mailto:robingilbert.deschepper@unipv.it>>
Date: Thursday, 4 January 2024 at 10:44
To: NEST User Mailing List
<users@nest-simulator.org<mailto:users@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@colorado.edu<mailto:anthonyylee@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@gmail.com<mailto:alvin.spivey@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
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_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
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--
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/
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NEST Users mailing list --
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To unsubscribe send an email to
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--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055