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

TVB-multiscale JupyterHub apps are now deprecated! See: https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/ about how to run TVB-multiscale (TVB-NEST, TVB-NetPyNE (NEURON), TVB-ANNarchy) on EBRAINS!

What can I find here?

• Presentation slides from the Summer School lecture on TVB-multiscale cosimulation (2021-06-07-McGill_VirtualCourse.pdf).
• Homework materials including a use case of a TVB - Spiking Basal Ganglia multiscale cosimulation notebook (see also attached .zip file at the current page)
• Homework solutions and Homework solutions' outputs (see also attached .zip files at the current page; password protected)
• The notebook BasalGanglia.ipynb used for the demonstration of this TVB-multiscale use case during the lecture.

Guide to run the use-case notebook

1. Run the TVB-Multiscale app by browsing to https://tvb-multiscale.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/McGillSummerSchool. All materials can also be found as the file Homework.zip attached to the current 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.
6. You can also run the lecture notebook BasalGanglia.ipynb in a similar manner, if you upload it to the same path where basal_ganglia_conn, and the pictures folder pics are.