22 Dec
2023
22 Dec
'23
8:45 p.m.
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
23 Dec
23 Dec
12:58 a.m.
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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
4 Jan
4 Jan
10:44 a.m.
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
_______________________________________________
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
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/
11:21 a.m.
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(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@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
_______________________________________________
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>
_______________________________________________
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>
--
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/
29 Mar
29 Mar
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
_______________________________________________
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
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
9 Apr
9 Apr
10:39 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
_______________________________________________
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>
_______________________________________________
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>
--
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@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>
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
23 Apr
23 Apr
7:02 a.m.
Hi Alvin,
You can use NEST simulator with the help of conda in google colab.
To do this, the package `condacolab`
(https://pypi.org/project/condacolab/) needs to be installed:
!pip install -q condacolab
import condacolab
condacolab.install()
Then you can use `conda` or `mamba`:
!mamba install -c conda-forge nest-simulator
NEST should now be usable:
import nest
nest.__version__
Best
Steffen
Am 09.04.24 um 22:39 schrieb Hans Ekkehard Plesser:
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
_______________________________________________
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>
_______________________________________________
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>
--
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@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>
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
--------------------------------------------------------------
Steffen Graber
Institute for Advanced Simulation (IAS-6), Computational and
Systems Neuroscience & JARA-Institute Brain Structure-Function
Relationships (INM-10)
Forschungszentrum Jülich GmbH
https://www.csn.fz-juelich.de
Forschungszentrum Jülich GmbH
Institute for Advanced Simulation
Jülich Supercomputing Centre (JSC)
Simulation & Data Lab Neuroscience
https://www.fz-juelich.de/en/ias/jsc/about-us/structure/simulation-and-data…
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
30 Apr
30 Apr
11:28 p.m.
Thanks Stephen,
That worked!
I assumed the same would be for nestml, but I get "NameError: name 'nestml'
is not defined" :
#Instructions from.)
https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installa…
import condacolab
condacolab.install()
!conda create --name wnestml
!conda activate wnestml
!conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt
wxpython boost boost-cpp libboost cmake make
!pip install nestml
import nestml
nestml.__version__
Suggestions?
Bests,
On Mon, Apr 22, 2024 at 10:02 PM Steffen Graber <s.graber(a)fz-juelich.de>
wrote:
Hi Alvin,
You can use NEST simulator with the help of conda in google colab.
To do this, the package `condacolab`
(https://pypi.org/project/condacolab/) needs to be installed:
!pip install -q condacolab
import condacolab
condacolab.install()
Then you can use `conda` or `mamba`:
!mamba install -c conda-forge nest-simulator
NEST should now be usable:
import nest
nest.__version__
Best
Steffen
Am 09.04.24 um 22:39 schrieb Hans Ekkehard Plesser:
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
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/outputfr…
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')
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/outputfr…
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(a)unipv.it
<mailto:robingilbert.deschepper@unipv.it>>
Date: Thursday, 4 January 2024 at 10:44
To: NEST User Mailing List <users(a)nest-simulator.org<mailtomailto:
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
<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(a)gmail.com<mailtomailto:
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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org<mailtolto:
users(a)nest-simulator.org>
To unsubscribe send an email to
users-leave(a)nest-simulator.org<mailtolto:
users-leave(a)nest-simulator.org>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org<mailtolto:
users(a)nest-simulator.org>
To unsubscribe send an email to
users-leave(a)nest-simulator.org<mailtolto:
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<mailtolto:
users(a)nest-simulator.org>
To unsubscribe send an email to
users-leave(a)nest-simulator.org<mailtolto:
users-leave(a)nest-simulator.org>
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
--------------------------------------------------------------
Steffen Graber
Institute for Advanced Simulation (IAS-6), Computational and
Systems Neuroscience & JARA-Institute Brain Structure-Function
Relationships (INM-10)
Forschungszentrum Jülich GmbH
https://www.csn.fz-juelich.de
Forschungszentrum Jülich GmbH
Institute for Advanced Simulation
Jülich Supercomputing Centre (JSC)
Simulation & Data Lab Neuroscience
https://www.fz-juelich.de/en/ias/jsc/about-us/structure/simulation-and-data…
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
11:37 p.m.
Hi,
Try importing "pynestml" instead.
You can find several examples of how to use NESTML here:
https://nestml.readthedocs.io/en/latest/tutorials/index.html
Thanks and let us know how you fare!
Kind regards,
Charl
On Tue, Apr 30, 2024, at 23:28, Alvin Spivey wrote:
Thanks Stephen,
That worked!
I assumed the same would be for nestml, but I get "NameError: name 'nestml'
is not defined" :
#Instructions from.)
https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installa…
import condacolab
condacolab.install()
!conda create --name wnestml
!conda activate wnestml
!conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt wxpython boost
boost-cpp libboost cmake make
!pip install nestml
import nestml
nestml.__version__
Suggestions?
Bests,
On Mon, Apr 22, 2024 at 10:02 PM Steffen Graber <s.graber(a)fz-juelich.de> wrote:
Hi Alvin,
You can use NEST simulator with the help of conda in google colab.
To do this, the package `condacolab`
(https://pypi.org/project/condacolab/) needs to be installed:
!pip install -q condacolab
import condacolab
condacolab.install()
Then you can use `conda` or `mamba`:
!mamba install -c conda-forge nest-simulator
NEST should now be usable:
import nest
nest.__version__
Best
Steffen
Am 09.04.24 um 22:39 schrieb Hans Ekkehard Plesser:
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
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
_______________________________________________
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>
_______________________________________________
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>
--
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@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>
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
--------------------------------------------------------------
Steffen Graber
Institute for Advanced Simulation (IAS-6), Computational and
Systems Neuroscience & JARA-Institute Brain Structure-Function
Relationships (INM-10)
Forschungszentrum Jülich GmbH
https://www.csn.fz-juelich.de
Forschungszentrum Jülich GmbH
Institute for Advanced Simulation
Jülich Supercomputing Centre (JSC)
Simulation & Data Lab Neuroscience
https://www.fz-juelich.de/en/ias/jsc/about-us/structure/simulation-and-data…
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
3 May
3 May
1:04 a.m.
This worked:
!pip install nestml
import pynestml
pynestml.__version__
Thank you everyone!
On Tue, Apr 30, 2024 at 2:45 PM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Hi,
Try importing "pynestml" instead.
You can find several examples of how to use NESTML here:
https://nestml.readthedocs.io/en/latest/tutorials/index.html
Thanks and let us know how you fare!
Kind regards,
Charl
On Tue, Apr 30, 2024, at 23:28, Alvin Spivey wrote:
Thanks Stephen,
That worked!
I assumed the same would be for nestml, but I get "NameError: name
'nestml' is not defined" :
#Instructions from.)
https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installa…
import condacolab
condacolab.install()
!conda create --name wnestml
!conda activate wnestml
!conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt
wxpython boost boost-cpp libboost cmake make
!pip install nestml
import nestml
nestml.__version__
Suggestions?
Bests,
On Mon, Apr 22, 2024 at 10:02 PM Steffen Graber <s.graber(a)fz-juelich.de>
wrote:
Hi Alvin,
You can use NEST simulator with the help of conda in google colab.
To do this, the package `condacolab`
(https://pypi.org/project/condacolab/) needs to be installed:
!pip install -q condacolab
import condacolab
condacolab.install()
Then you can use `conda` or `mamba`:
!mamba install -c conda-forge nest-simulator
NEST should now be usable:
import nest
nest.__version__
Best
Steffen
Am 09.04.24 um 22:39 schrieb Hans Ekkehard Plesser:
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
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/outputfr…
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')
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/outputfr…
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(a)unipv.it
<mailto:robingilbert.deschepper@unipv.it>>
Date: Thursday, 4 January 2024 at 10:44
To: NEST User Mailing List <users(a)nest-simulator.org<mailtomailto:
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
<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(a)gmail.com<mailtomailto:
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
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org<mailtolto:
users(a)nest-simulator.org>
To unsubscribe send an email to
users-leave(a)nest-simulator.org<mailtolto:
users-leave(a)nest-simulator.org>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org<mailtolto:
users(a)nest-simulator.org>
To unsubscribe send an email to
users-leave(a)nest-simulator.org<mailtolto:
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<mailtolto:
users(a)nest-simulator.org>
To unsubscribe send an email to
users-leave(a)nest-simulator.org<mailtolto:
users-leave(a)nest-simulator.org>
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
--------------------------------------------------------------
Steffen Graber
Institute for Advanced Simulation (IAS-6), Computational and
Systems Neuroscience & JARA-Institute Brain Structure-Function
Relationships (INM-10)
Forschungszentrum Jülich GmbH
https://www.csn.fz-juelich.de
Forschungszentrum Jülich GmbH
Institute for Advanced Simulation
Jülich Supercomputing Centre (JSC)
Simulation & Data Lab Neuroscience
https://www.fz-juelich.de/en/ias/jsc/about-us/structure/simulation-and-data…
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
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NEST Users mailing list -- users(a)nest-simulator.org
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Alvin J. Spivey, Ph.D.
(c) 843.267.8055
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1:11 a.m.
For completeness,
The full Google Colab installation:
loading = False
from google.colab import drive
drive.mount('/content/drive')
!pip install -q condacolab
import condacolab
condacolab.install()
!conda install -c conda-forge nest-simulator
import nest
nest.__version__
!pip install nestml
import pynestml
pynestml.__version__
On Thu, May 2, 2024 at 4:04 PM Alvin Spivey <alvin.spivey(a)gmail.com> wrote:
This worked:
!pip install nestml
import pynestml
pynestml.__version__
Thank you everyone!
On Tue, Apr 30, 2024 at 2:45 PM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
Hi,
Try importing "pynestml" instead.
You can find several examples of how to use NESTML here:
https://nestml.readthedocs.io/en/latest/tutorials/index.html
Thanks and let us know how you fare!
Kind regards,
Charl
On Tue, Apr 30, 2024, at 23:28, Alvin Spivey wrote:
Thanks Stephen,
That worked!
I assumed the same would be for nestml, but I get "NameError: name
'nestml' is not defined" :
#Instructions from.)
https://nestml.readthedocs.io/en/latest/installation.html#anaconda-installa…
import condacolab
condacolab.install()
!conda create --name wnestml
!conda activate wnestml
!conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt
wxpython boost boost-cpp libboost cmake make
!pip install nestml
import nestml
nestml.__version__
Suggestions?
Bests,
On Mon, Apr 22, 2024 at 10:02 PM Steffen Graber <s.graber(a)fz-juelich.de>
wrote:
Hi Alvin,
You can use NEST simulator with the help of conda in google colab.
To do this, the package `condacolab`
(https://pypi.org/project/condacolab/) needs to be installed:
!pip install -q condacolab
import condacolab
condacolab.install()
Then you can use `conda` or `mamba`:
!mamba install -c conda-forge nest-simulator
NEST should now be usable:
import nest
nest.__version__
Best
Steffen
Am 09.04.24 um 22:39 schrieb Hans Ekkehard Plesser:
--
Alvin J. Spivey, Ph.D.
(c) 843.267.8055
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/outputfr…
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')
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/outputfr…
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(a)nmbu.no<mailtolto:
hans.ekkehard.plesser(a)nmbu.no>
Home http://arken.nmbu.no/~plesser
From: Robin Gilbert De Schepper <robingilbert.deschepper(a)unipv.it
<mailto:robingilbert.deschepper@unipv.it>>
Date: Thursday, 4 January 2024 at 10:44
To: NEST User Mailing List <users(a)nest-simulator.org<mailtomailto:
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
<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(a)gmail.com<mailtomailto:
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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>
>
> --
> 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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--
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(c) 843.267.8055
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--
--------------------------------------------------------------
Steffen Graber
Institute for Advanced Simulation (IAS-6), Computational and
Systems Neuroscience & JARA-Institute Brain Structure-Function
Relationships (INM-10)
Forschungszentrum Jülich GmbH
https://www.csn.fz-juelich.de
Forschungszentrum Jülich GmbH
Institute for Advanced Simulation
Jülich Supercomputing Centre (JSC)
Simulation & Data Lab Neuroscience
https://www.fz-juelich.de/en/ias/jsc/about-us/structure/simulation-and-data…
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
Forschungszentrum Jülich GmbH
52425 Jülich
Sitz der Gesellschaft: Jülich
Eingetragen im Handelsregister des Amtsgerichts Düren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Stefan Müller
Geschäftsführung: Prof. Dr. Astrid Lambrecht (Vorsitzende),
Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens
---------------------------------------------------------------------------------------------
---------------------------------------------------------------------------------------------
_______________________________________________
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
_______________________________________________
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To unsubscribe send an email to users-leave(a)nest-simulator.org
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10 comments
6 participants
participants (6)
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Alvin Spivey -
Anthony Lee -
Charl Linssen -
Hans Ekkehard Plesser -
Robin Gilbert De Schepper -
Steffen Graber