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From version 31.1
edited by dionperd
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To version 37.1
edited by dionperd
on 2024/04/08 12:51
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7 7  August 9th, 2022
8 8  
9 9  
10 +== (% 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!(%%)** ==
11 +
12 +
13 +=== What can I find here? ===
14 +
15 +* [[Presentation slides>>attach:2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf]] from the course's lecture.
16 +* Materials recommended for further study
17 +* Guid to run the notebook TVB-NEST co-simulation demonstrated in the course.
18 +
19 +=== ===
20 +
10 10  === Recommendation for self-study ===
11 11  
12 12  * [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
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15 15  [[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]]
16 16  )))
17 17  
29 +=== ===
18 18  
19 -=== What can I find here? ===
31 +=== Guide to run the course's notebook ===
20 20  
21 -* Presentation slides from the course's lecture.
22 -* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
33 +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!)
34 +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.
35 +1. Run the WilsonCowan.ipynb notebook.
23 23  
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 -
32 32  == ==
2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf
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1 +XWiki.dionperd
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