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Last modified by dionperd on 2024/04/08 12:54
From version 1.1
edited by dionperd
on 2022/08/05 12:19
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To version 31.1
edited by dionperd
on 2022/11/08 16:54
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1 -TheVirtual BrainInClinicalResearchAugust2022
1 +The Virtual Brain In Clinical Research August 2022
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2 -== [[image:https://www.brainsimulation.org/bsw/img/9687/text_illustration_maxi@2x||alt="Virtual Course Series Summer 2022 Banner"]] ==
1 +== ==
3 3  
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5 -== **The Virtual Brain in Clinical Research: An Introduction**. Charite, June 28th, 2022 to September 13th, 2022 ==
3 +[[image:VirtualBrainClinicalResearch.png]]
6 6  
5 +== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
6 +
7 +August 9th, 2022
8 +
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 +=== What can I find here? ===
20 +
21 +* Presentation slides from the course's lecture.
22 +* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
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 +
7 7  == ==
VirtualBrainClinicalResearch.png
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