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1 -Simulate with EBRAINS TVB-multiscale workshop presentation (November 2022)
1 +The Virtual Brain In Clinical Research August 2022
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1 -== [[image:SimulateWithEBRAINS.jpg]] ==
1 +== ==
2 2  
3 +[[image:VirtualBrainClinicalResearch.png]]
3 3  
4 -(% class="wikigeneratedid" id="HTheVirtualBraininClinicalResearch:AnIntroduction.Charite2CA0June28th2C2022toSeptember13th2C2022" %)
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  
10 +=== Recommendation for self-study ===
11 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 +
12 12  === What can I find here? ===
13 13  
14 -* Presentation slides from the workshop's lecture.
15 -* The notebook demonstrated during the workshop.
21 +* Presentation slides from the course's lecture.
22 +* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
16 16  
24 +
17 17  === Guide to run the use-case notebook ===
18 18  
19 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 20  1. Navigate to "Contributed-Notebooks" folder, which offers user-specific persistent storage.
21 -1. Unzip there 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..
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.
23 23  
24 24  == ==
SimulateWithEBRAINS.zip
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VirtualBrainClinicalResearch.png
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