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From version 30.1
edited by dionperd
on 2022/11/08 16:45
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1 -== [[image:SimulateWithEBRAINS.jpg]] ==
1 +== ==
2 2  
3 +[[image:VirtualBrainClinicalResearch.png]]
3 3  
4 -== **TVB-Multiscale: Deep Brain Stimulation use case demonstration** ==
5 +== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
5 5  
6 -(% class="wikigeneratedid" %)
7 -November 9th, 2022
7 +August 9th, 2022
8 8  
9 9  
10 -
11 11  === What can I find here? ===
12 12  
13 -* Presentation slides from the workshop's lecture.
14 -* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
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.
15 15  
16 -=== Guide to run the use-case notebook ===
17 17  
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.
17 +=== Recommendation for self-study ===
22 22  
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 +
23 23  == ==