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1 -== ==
1 +== [[image:SimulateWithEBRAINS.jpg]] ==
2 2  
3 -[[image:VirtualBrainClinicalResearch.png]]
4 4  
5 -== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
4 +== **TVB-Multiscale: Deep Brain Stimulation use case demonstration** ==
6 6  
7 -August 9th, 2022
6 +(% class="wikigeneratedid" %)
7 +November 9th, 2022
8 8  
9 9  
10 +
10 10  === What can I find here? ===
11 11  
12 -* Presentation slides from the course's lecture.
13 -* Materials recommended for further study
14 -* Guid to run the notebook TVB-NEST co-simulation demonstrated in the course.
13 +* Presentation slides from the workshop's lecture.
14 +* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
15 15  
16 +=== Guide to run the use-case notebook ===
16 16  
17 -=== Recommendation for self-study ===
18 +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!)
19 +1. Navigate to "Contributed-Notebooks" folder, which offers user-specific persistent storage.
20 +1. Upload and unzip there [[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]] by starting a terminal session or a new notebook and running unzip SimulateWithEBRAINS.zip
21 +1. Run the TVB-corr-cortex-opt.ipynb notebook for TVB-ANNarchy cosimulation and the ANNarchy-spiking-cortex.ipynb one for ANNarchy only simulation.
18 18  
19 -* [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
20 -* [[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]]
21 -* (((
22 -[[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]]
23 -)))
24 -
25 -=== ===
26 -
27 -
28 -=== Guide to run the course's notebook ===
29 -
30 -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!)
31 -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.
32 -1. Run the WilsonCowan.ipynb notebook.
33 -
34 34  == ==
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