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TVB-multiscale-cosim_McGillSummerSchool_06-2021

Version 31.1 by dionperd on 2021/05/28 20:15

Course on TVB-multiscale cosimulation

McGill University "Summer School in Nonlinear Dynamics for the Life Sciences with Applications to Neuroscience and Psychology" (June 2021)

What can I find here?

  • Homework materials including a use case of a TVB - Spiking Basal Ganglia multiscale cosimulation (see also attached .zip file below)
  • Homework solutions (see also attached .zip file below; password protected)

Who has access?

Everybody with an EBRAINS account.

Guide to run the use-case notebook

  1. Run the TVB-NEST app by browsing to https://tvb-nest.apps.hbp.eu/ and logging in with your EBRAINS account.
  2. Navigate to "ContributedNotebooks" folder, which offers persistent storage for EBRAINS users.
  3. You will need the notebook BasalGangliaHomework.ipynb, the data folder basal_ganglia_conn, and the pictures folder pics, found in the drive folder "Homework. All materials can also be found as a .zip file "Homework.zip" attached to this page (scroll down to find it).
  4. The easiest way to get the above materials is to upload "Homework.zip" to "ContributedNotebooks" folder, and run the command
    ! unzip ./Homework.zip
    on a cell of a new notebook, from within the same folder.
  5. 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.
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