Attention: The EBRAINS drive will be unavailable for most of the weekend starting the 25th October. Although the Lab is availble while the Drive is down, files that are stored in the Drive will not be loaded and you will be unable to save documents directly on the Lab.


Last modified by dionperd on 2024/04/08 12:54
From version 3.1
edited by dionperd
on 2022/08/05 12:29
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To version 29.1
edited by dionperd
on 2022/11/08 16:02
Change comment: Deleted attachment "SimulateWithEBRAINS.zip"

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1 -TheVirtual BrainInClinicalResearchAugust2022
1 +The Virtual Brain In Clinical Research August 2022
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1 -(% class="wikigeneratedid" %)
2 -== [[image:https://www.brainsimulation.org/bsw/img/9687/text_illustration_maxi@2x||alt="Virtual Course Series Summer 2022 Banner"]] ==
1 +== [[image:SimulateWithEBRAINS.jpg]] ==
3 3  
4 -(% class="wikigeneratedid" id="HTheVirtualBraininClinicalResearch:AnIntroduction.Charite2CA0June28th2C2022toSeptember13th2C2022" %)
5 -**The Virtual Brain in Clinical Research: An Introduction**.
6 6  
4 +== **TVB-Multiscale: Deep Brain Stimulation use case demonstration** ==
5 +
7 7  (% class="wikigeneratedid" %)
8 -Charite, June 28th, 2022 to September 13th, 2022
7 +November 9th, 2022
9 9  
10 10  
11 11  
12 -== What can I find here? ==
11 +=== What can I find here? ===
13 13  
14 -* Presentation slides from course's lecture: [[**Week 7 “The Virtual Brain and multiscale co-simulation” **– Dr. Dionysios Perdikis>>https://www.dropbox.com/s/vqjgajteqpg5ofx/2022-08-09_TVB-multiscale_SummerVirtualCourse.pptx?dl=0]].
13 +* Presentation slides from the workshop's lecture.
14 +* The notebook ([[SimulateWithEBRAINS.zip>>attach:SimulateWithEBRAINS.zip]]) demonstrated during the workshop.
15 15  
16 16  === Guide to run the use-case notebook ===
17 17  
18 -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!)
19 -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.
20 -1. Run the WilsonCowan.ipynb notebook.
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.
21 21  
22 -== ==
23 +== ==