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1 -The Virtual Brain in Clinical Research. An Introduction. (August 2022)
1 +The Virtual Brain In Clinical Research August 2022
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1 -== [[image:https://www.brainsimulation.org/bsw/img/9687/text_illustration_maxi@2x||alt="Virtual Course Series Summer 2022 Banner"]] ==
1 +== ==
2 2  
3 -(% class="wikigeneratedid" id="HTheVirtualBraininClinicalResearch:AnIntroduction.Charite2CA0June28th2C2022toSeptember13th2C2022" %)
4 -**The Virtual Brain in Clinical Research: An Introduction**.
3 +[[image:VirtualBrainClinicalResearch.png]]
5 5  
6 -(% class="wikigeneratedid" %)
7 -Charite, June 28th, 2022 to September 13th, 2022
5 +== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
8 8  
7 +August 9th, 2022
9 9  
10 10  
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 +
11 11  === What can I find here? ===
12 12  
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]](%%).
21 +* Presentation slides from the course's lecture.
22 +* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
14 14  
24 +
15 15  === Guide to run the use-case notebook ===
16 16  
17 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.
19 -1. Run the WilsonCowan.ipynb notebook.
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.
20 20  
21 21  == ==
2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf
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