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  • 2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf
  • VirtualBrainClinicalResearch.png

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1		-== [[image:SimulateWithEBRAINS.jpg]] ==
	1	+== ==
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	3	+[[image:VirtualBrainClinicalResearch.png]]
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4		-== **TVB-Multiscale: Deep Brain Stimulation use case demonstration** ==
	5	+== **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** ==
5	5
	7	+August 9th, 2022
	8	+
	9	+
	10	+=== What can I find here? ===
	11	+
	12	+* [[Presentation slides>>attach:2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf]] 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	+
6	6	(% class="wikigeneratedid" %)
7		-November 9th, 2022
	17	+=== ===
8	8
	19	+=== Recommendation for self-study ===
9	9
	21	+* [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]]
	22	+* [[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]]
	23	+* (((
	24	+[[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]]
	25	+)))
10	10
11		-=== What can I find here? ===
	27	+=== ===
12	12
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 ===
	30	+=== Guide to run the course's 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.
	32	+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!)
	33	+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.
	34	+1. Run the WilsonCowan.ipynb notebook.
22	22
23	23	== ==

2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf

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VirtualBrainClinicalResearch.png

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