Wiki source code of The Virtual Brain In Clinical Research August 2022
Last modified by dionperd on 2024/04/08 12:54
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| 1 | == == | ||
| 2 | |||
| 3 | [[image:VirtualBrainClinicalResearch.png]] | ||
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| 5 | == **Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis** == | ||
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| 7 | August 9th, 2022 | ||
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| 10 | (% class="wikigeneratedid" id="HTVB-multiscaleJupyterHubappsarenowdeprecated21See:https:2F2Fwiki.ebrains.eu2Fbin2Fview2FCollabs2Fthe-virtual-brain-multiscale2FA0abouthowtorunTVB-multiscale28TVB-NEST2CTVB-NetPyNE28NEURON292CTVB-ANNarchy29onEBRAINS21" %) | ||
| 11 | (% 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!(%%)** | ||
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| 13 | |||
| 14 | === What can I find here? === | ||
| 15 | |||
| 16 | * [[Presentation slides>>attach:2022-08-09_TVB-multiscale_SummerVirtualCourse.pdf]] from the course's lecture. | ||
| 17 | * Materials recommended for further study | ||
| 18 | * Guid to run the notebook TVB-NEST co-simulation demonstrated in the course. | ||
| 19 | |||
| 20 | === === | ||
| 21 | |||
| 22 | === Recommendation for self-study === | ||
| 23 | |||
| 24 | * [[TVB advanced tutorials>>https://training.incf.org/course/virtual-brain-node-6-workshop]] | ||
| 25 | * [[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]] | ||
| 26 | * ((( | ||
| 27 | [[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]] | ||
| 28 | ))) | ||
| 29 | |||
| 30 | === === | ||
| 31 | |||
| 32 | === Guide to run the course's notebook === | ||
| 33 | |||
| 34 | 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!) | ||
| 35 | 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. | ||
| 36 | 1. Run the WilsonCowan.ipynb notebook. | ||
| 37 | |||
| 38 | == == |