Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time


Last modified by dionperd on 2024/04/08 12:54
From version 38.1
edited by dionperd
on 2024/04/08 12:54
Change comment: There is no comment for this version
To version 31.1
edited by dionperd
on 2022/11/08 16:54
Change comment: There is no comment for this version

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7 7  August 9th, 2022
8 8  
9 9  
10 -(% class="wikigeneratedid" id="HTVB-multiscaleJupyterHubappsarenowdeprecated21See:https:2F2Fwiki.ebrains.eu2Fbin2Fview2FCollabs2Fthe-virtual-brain-multiscale2FA0abouthowtorunTVB-multiscale28TVB-NEST2CTVB-NetPyNE28NEURON292CTVB-ANNarchy29onEBRAINS21" %)
11 -(% style="color:#e74c3c" %)**TVB-multiscale JupyterHub apps are now deprecated! See:** (%%)**[[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/]] (% style="color:#e74c3c" %)about how to run TVB-multiscale (TVB-NEST, TVB-NetPyNE (NEURON), TVB-ANNarchy) on EBRAINS!(%%)**
12 -
13 -
14 -=== What can I find here? ===
15 -
16 -* [[Presentation slides>>attach:2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf]] from the course's lecture.
17 -* Materials recommended for further study
18 -* Guid to run the notebook TVB-NEST co-simulation demonstrated in the course.
19 -
20 -=== ===
21 -
22 22  === Recommendation for self-study ===
23 23  
24 24  * [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
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27 27  [[Sanz-Leon, P., Knock, S. A., Spiegler, A., & Jirsa, V. K. (2015). Mathematical framework for large-scale brain network modeling in The Virtual Brain. Neuroimage>>https://www.sciencedirect.com/science/article/pii/S1053811915000051]]
28 28  )))
29 29  
30 -=== ===
31 31  
32 -=== Guide to run the course's notebook ===
19 +=== What can I find here? ===
33 33  
34 -1. Run the EBRAINS TVB-Multiscale app by browsing to [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>url:https://tvb-multiscale.apps.hbp.eu/]] and logging in with your EBRAINS account. (The first time you log-in, you might need to try several times by refreshing the page, until it works for you!)
35 -1. Navigate to "TVB-Multiscale-Examples/documented_example_notebooks" folder, and upload the [[WilsonCowan.ipynb notebook>>path:/bin/download/Collabs/tvb-multiscale-cosim-mcgillsummerschool/INCF%20Neuroinformatics%20Assembly%202022%20training%20workshop.%20Enabling%20multi-scale%20data%20integration%3A%20Turning%20data%20to%20knowledge./WebHome/WilsonCowan.ipynb?rev=1.1]], to the "Contributed-Notebooks" folder, which offers user-specific persistent storage.
36 -1. Run the WilsonCowan.ipynb notebook.
21 +* Presentation slides from the course's lecture.
22 +* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
37 37  
24 +
25 +=== Guide to run the use-case notebook ===
26 +
27 +1. Run the EBRAINS TVB-Multiscale app by browsing to [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>https://tvb-multiscale.apps.hbp.eu/]] and logging in with your EBRAINS account. (The first time you log-in, you might need to try several times by refreshing the page, until it works for you!)
28 +1. Navigate to "Contributed-Notebooks" folder, which offers user-specific persistent storage.
29 +1. Upload and unzip there [[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]] by starting a terminal session or a new notebook and running unzip SimulateWithEBRAINS.zip
30 +1. Run the TVB-corr-cortex-opt.ipynb notebook for TVB-ANNarchy cosimulation and the ANNarchy-spiking-cortex.ipynb one for ANNarchy only simulation.
31 +
38 38  == ==
2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf
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1 -XWiki.dionperd
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1 -14.2 MB
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