Wiki source code of 5th TVB in EBRAINS TVB-multiscale cosimulation hands-on session
Last modified by dionperd on 2024/04/08 12:54
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28.1 | 1 | (% class="wikigeneratedid" id="HTVB-multiscaleJupyterHubappsarenowdeprecated21See:A0https:2F2Fwiki.ebrains.eu2Fbin2Fview2FCollabs2Fthe-virtual-brain-multiscale2FA0abouthowtorunTVB-multiscale28TVB-NEST2CTVB-NetPyNE28NEURON292CTVB-ANNarchy29onEBRAINS21" %) |
| 2 | (% 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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26.1 | 5 | === What can I find here? === |
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2.1 | 6 | |
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18.1 | 7 | * Presentation slides from the workshop's introductory lecture on TVB-multiscale cosimulation ([[2021-06-04-5thTVBinEBRAINSworkshlp.pdf>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/5thTVBinEBRAINSworkshop/2021-06-04-5thTVBinEBRAINSworkshlp.pdf]]). |
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10.1 | 8 | * 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 |
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23.1 | 9 | * A Jupyter notebook [[BasalHomeworkSolved.ipynb>>https://drive.ebrains.eu/lib/14db5dbf-97c8-4971-86e5-9b15fd57dd87/file/5thTVBinEBRAINSworkshop/BasalGangliaSolved.ipynb]] with all the solutions to the session, which will be posted right after the session is over. |
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| 11 | === Guide to run the use-case notebook === | ||
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25.1 | 13 | 1. Run the 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. |
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1.1 | 14 | 1. Navigate to "ContributedNotebooks" folder, which offers persistent storage for EBRAINS users. |
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17.1 | 15 | 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 at the file [[HandsOn.zip>>https://wiki.ebrains.eu/bin/download/Collabs/tvb-multiscale-cosim-mcgillsummerschool/4th%20TVB%20in%20EBRAINS%20TVB-multiscale%20cosimulation%20hands-on%20session/WebHome/HandsOn.zip?rev=1.1]] attached to the current page (scroll down to find it). |
| 16 | 1. The easiest way to get the above materials is to upload HandsOn.zip to "ContributedNotebooks" folder, and run the command | ||
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15.1 | 17 | ! unzip ./HandsOn.zip |
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1.1 | 18 | on a cell of a new notebook, from within the same folder. |
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10.1 | 19 | 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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