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1 -The Virtual Brain In Clinical Research August 2022
1 +The Virtual Brain in Clinical Research. An Introduction. (August 2022)
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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 -=== Recommendation for self-study ===
11 -
12 -* [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
13 -* [[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]]
14 -* (((
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 -)))
17 -
18 -
19 19  === What can I find here? ===
20 20  
21 -* Presentation slides from the course's lecture.
22 -* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
13 +* Presentation slides from course's lecture: [[(% class="wikiattachmentlink wikiattachmentlink" %)**Week 7 “The Virtual Brain and multiscale co-simulation” **– Dr. Dionysios Perdikis>>attach:2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf]](%%).
23 23  
24 -
25 25  === Guide to run the use-case notebook ===
26 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.
17 +1. Run the EBRAINS TVB-NEST development app by browsing to [[https:~~/~~/tvb-nest-dev.apps.hbp.eu/>>https://tvb-nest-dev.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-NEST-Examples/documented_example_notebooks" folder, and copy paste the WilsonCowan.ipynb notebook, upwards to the "Contributed-Notebooks" folder, which offers user-specific persistent storage.
19 +1. Run the WilsonCowan.ipynb notebook.
31 31  
32 -== ==
21 +== ==
VirtualBrainClinicalResearch.png
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2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf
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