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Last modified by dionperd on 2024/04/08 12:54
From version 7.2
edited by dionperd
on 2021/06/02 16:18
Change comment: Update document after refactoring.
To version 10.1
edited by dionperd
on 2021/06/02 16:32
Change comment: There is no comment for this version

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1 -4th TVB in EBRAINS TVB-multiscale cosimulation hands-on session
1 +5th TVB in EBRAINS TVB-multiscale cosimulation hands-on session
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2 -//McGill University "Summer School in Nonlinear Dynamics for the Life Sciences with Applications to Neuroscience and Psychology" (June 2021)//
2 +What can I find here?
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4 -== What can I find here? ==
4 +* A Jupyter notebook [[BasalGanglia.ipynb>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/5thTVBinEBRAINSworkshop/BasalGanglia.ipynb]] used for the hands-on session
5 +* A Jupyter notebook BasalHomeworkSolved.ipynb with all the solutions to the session, which will be posted right after the session is over.
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6 -* [[Homework materials>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework]] including a use case of a TVB - Spiking Basal Ganglia multiscale cosimulation notebook (see also attached .zip file at the current page)
7 -* [[Homework solutions>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/MacGillSummerSchool/HomeworkSolutions.zip]] and [[Homework solutions' outputs>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/MacGillSummerSchool/HomeworkSolutionsOutputs.zip]] (see also attached .zip files at the current page; password protected)
8 -
9 9  === Guide to run the use-case notebook ===
10 10  
11 11  1. Run the TVB-NEST app by browsing to [[https:~~/~~/tvb-nest.apps.hbp.eu/>>url:https://tvb-nest.apps.hbp.eu/]] and logging in with your EBRAINS account.
12 12  1. Navigate to "ContributedNotebooks" folder, which offers persistent storage for EBRAINS users.
13 -1. You will need the notebook [[BasalGangliaHomework.ipynb>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/MacGillSummerSchool/Homework/BasalGangliaHomework.ipynb]], the data folder [[basal_ganglia_conn>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework/basal_ganglia_conn]], and the pictures folder [[pics>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework/pics]], found in the [[drive folder "Homework/McGillSummerSchool>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/MacGillSummerSchool/Homework]]. All materials can also be found as a .zip file "Homework.zip" attached to the current page (scroll down to find it).
14 -1. The easiest way to get the above materials is to upload "Homework.zip" to "ContributedNotebooks" folder, and run the command
11 +1. You will need the notebook [[BasalGanglia.ipynb>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/5thTVBinEBRAINSworkshop/BasalGanglia.ipynb]], the data folder [[basal_ganglia_conn>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/5thTVBinEBRAINSworkshop/basal_ganglia_conn]], and the pictures folder [[pics>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/5thTVBinEBRAINSworkshop/pics]], found in the [[drive folder "5thTVBinEBRAINSworkshop>>https://drive.ebrains.eu/#my-libs/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/5thTVBinEBRAINSworkshop]]. All materials can also be found as a .zip file "HandsOn.zip" attached to the current page (scroll down to find it).
12 +1. The easiest way to get the above materials is to upload "HandsOn.zip" to "ContributedNotebooks" folder, and run the command
15 15  ! unzip ./Homework.zip
16 16  on a cell of a new notebook, from within the same folder.
17 -1. Finally, navigate inside the decompressed Homework folder and run the notebook BasalGangliaHomework.ipynb. Your results will be saved in your personal drive space and can be found in the "ContributedNotebooks" folder whenever you log in again to the app.
15 +1. Finally, navigate inside the decompressed HandsOn folder and run the notebook BasalGanglia.ipynb. Your results will be saved in your personal drive space and can be found in the "ContributedNotebooks" folder whenever you log in again to the app.
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