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1 -The Virtual Brain In Clinical Research August 2022
1 +The Virtual Brain in Clinical Research. An Introduction. (August 2022)
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1 -== ==
1 +== [[image:https://www.brainsimulation.org/bsw/img/9687/text_illustration_maxi@2x||alt="Virtual Course Series Summer 2022 Banner"]] ==
2 2  
3 -[[image:VirtualBrainClinicalResearch.png]]
3 +(% class="wikigeneratedid" id="HTheVirtualBraininClinicalResearch:AnIntroduction.Charite2CA0June28th2C2022toSeptember13th2C2022" %)
4 +**The Virtual Brain in Clinical Research: An Introduction**.
4 4  
5 -== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
6 +(% class="wikigeneratedid" %)
7 +Charite, June 28th, 2022 to September 13th, 2022
6 6  
7 -August 9th, 2022
8 8  
9 9  
10 -== (% style="color:#e74c3c" %)**TVB-multiscale JupyterHub apps are now deprecated! See:** (%%)**[[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/]] (% style="color:#e74c3c" %)about how to run TVB-multiscale (TVB-NEST, TVB-NetPyNE (NEURON), TVB-ANNarchy) on EBRAINS!(%%)** ==
11 -
12 -
13 13  === What can I find here? ===
14 14  
15 -* [[Presentation slides>>attach:2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf]] from the course's lecture.
16 -* Materials recommended for further study
17 -* Guid to run the notebook TVB-NEST co-simulation demonstrated in the course.
13 +* Presentation slides from course's lecture: [[**Week 7 “The Virtual Brain and multiscale co-simulation” **– Dr. Dionysios Perdikis>>https://www.dropbox.com/s/7qt86f88txp0j9y/2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf?dl=0]].
18 18  
19 -=== ===
15 +== Guide to run the use-case notebook ==
20 20  
21 -=== Recommendation for self-study ===
22 -
23 -* [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
24 -* [[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]]
25 -* (((
26 -[[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]]
27 -)))
28 -
29 -=== ===
30 -
31 -=== Guide to run the course's notebook ===
32 -
33 -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!)
34 -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.
17 +1. Run the EBRAINS TVB-NEST development app by browsing to [[https:~~/~~/tvb-nest-dev.apps.hbp.eu/>>url:https://tvb-nest.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-NEST-Examples/documented_example_notebooks" folder, and copy paste the WilsonCowan.ipynb notebookt, upwards to the "Contributed-Notebooks" folder, which offers user-specific persistent storage.
35 35  1. Run the WilsonCowan.ipynb notebook.
36 36  
37 -== ==
21 +== ==
2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf
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