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 19.1
edited by dionperd
on 2022/11/08 15:37
Change comment: Uploaded new attachment "SimulateWithEBRAINS.jpg", version {1}

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -The Virtual Brain In Clinical Research August 2022
1 +The Virtual Brain in Clinical Research. An Introduction. (August 2022)
Content
... ... @@ -1,38 +1,21 @@
1 -== ==
1 +== [[image:https://www.brainsimulation.org/bsw/img/9687/text_illustration_maxi@2x||alt="Virtual Course Series Summer 2022 Banner"]] ==
2 2  
3 -[[image:VirtualBrainClinicalResearch.png]]
3 +(% class="wikigeneratedid" id="HTheVirtualBraininClinicalResearch:AnIntroduction.Charite2CA0June28th2C2022toSeptember13th2C2022" %)
4 +**The Virtual Brain in Clinical Research: An Introduction**.
4 4  
5 -== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
6 +(% class="wikigeneratedid" %)
7 +Charite, June 28th, 2022 to September 13th, 2022
6 6  
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 14  === What can I find here? ===
15 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.
13 +* Presentation slides from course's lecture: [[(% class="wikiattachmentlink wikiattachmentlink wikiattachmentlink wikiattachmentlink wikiattachmentlink" %)**Week 7 “The Virtual Brain and multiscale co-simulation” **– Dr. Dionysios Perdikis>>attach:2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf]](%%).
19 19  
20 -=== ===
15 +=== Guide to run the use-case notebook ===
21 21  
22 -=== Recommendation for self-study ===
23 -
24 -* [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
25 -* [[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]]
26 -* (((
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 -)))
29 -
30 -=== ===
31 -
32 -=== Guide to run the course's notebook ===
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.
17 +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!)
18 +1. Navigate to "TVB-Multiscale-Examples/documented_example_notebooks" folder, and copy paste the WilsonCowan.ipynb notebook, upwards to the "Contributed-Notebooks" folder, which offers user-specific persistent storage.
36 36  1. Run the WilsonCowan.ipynb notebook.
37 37  
38 38  == ==
VirtualBrainClinicalResearch.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.dionperd
Size
... ... @@ -1,1 +1,0 @@
1 -797.2 KB
Content
SimulateWithEBRAINS.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.dionperd
Size
... ... @@ -1,0 +1,1 @@
1 +387.5 KB
Content