Last modified by dionperd on 2024/04/08 12:54
From version 26.1
edited by dionperd
on 2022/11/08 15:47
Change comment: There is no comment for this version
To version 32.1
edited by dionperd
on 2022/11/08 16:57
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -Simulate with EBRAINS TVB-multiscale workshop presentation (November 2022)
1 +The Virtual Brain In Clinical Research August 2022
Content
... ... @@ -1,24 +1,34 @@
1 -(% class="wikigeneratedid" %)
2 -== [[image:SimulateWithEBRAINS.jpg]] ==
1 +== ==
3 3  
3 +[[image:VirtualBrainClinicalResearch.png]]
4 4  
5 -== **TVB-Multiscale: Deep Brain Stimulation use case demonstration** ==
5 +== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
6 6  
7 -(% class="wikigeneratedid" %)
8 -November 9th, 2022
7 +August 9th, 2022
9 9  
10 10  
11 -
12 12  === What can I find here? ===
13 13  
14 -* Presentation slides from the workshop's lecture.
15 -* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
12 +* Presentation slides from the course's lecture.
13 +* Materials recommended for further study
14 +* Guid to run the notebook TVB-NEST co-simulation demonstrated in the course.
16 16  
17 -=== Guide to run the use-case notebook ===
18 18  
19 -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!)
20 -1. Navigate to "Contributed-Notebooks" folder, which offers user-specific persistent storage.
21 -1. Upload and unzip there [[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]] by starting a terminal session or a new notebook and running unzip SimulateWithEBRAINS.zip
22 -1. Run the TVB-corr-cortex-opt.ipynb notebook for TVB-ANNarchy cosimulation and the ANNarchy-spiking-cortex.ipynb one for ANNarchy only simulation.
17 +=== Recommendation for self-study ===
23 23  
19 +* [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
20 +* [[Schirner, Domide, Perdikis, Triebkorn, Stefanovski, Pai, Prodan, Valean, Palmer, Langford, Blickensdörfer, van der Vlag, Diaz-Pier, Peyser, Woodman, Zehl, Fousek, Petkoski, Kusch, Hashemi, Marinazzo, Mangin, Flöel, Akintoye, Stahl, Deco, McIntosh, Hilgetag, Morgan, Schuller, Upton, McMurtrie, Dickscheid, Bjaalie, Amunts, Mersmann, Jirsa, Ritter (2022). Brain Simulation as a Cloud Service: The Virtual Brain on the European Research Platform EBRAINS. Neuroimage>>https://www.sciencedirect.com/science/article/pii/S1053811922001021]]
21 +* (((
22 +[[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]]
23 +)))
24 +
25 +=== ===
26 +
27 +
28 +=== Guide to run the course's notebook ===
29 +
30 +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!)
31 +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.
32 +1. Run the WilsonCowan.ipynb notebook.
33 +
24 24  == ==
SimulateWithEBRAINS.jpg
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.dionperd
Size
... ... @@ -1,1 +1,0 @@
1 -387.5 KB
Content
SimulateWithEBRAINS.zip
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.dionperd
Size
... ... @@ -1,1 +1,0 @@
1 -387.5 KB
Content
VirtualBrainClinicalResearch.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.dionperd
Size
... ... @@ -1,0 +1,1 @@
1 +797.2 KB
Content