Week 7 “The Virtual Brain and multiscale co-simulation” – Dr. Dionysios Perdikis

August 9th, 2022

Recommendation for self-study

• TVB advanced tutorials
• Schirner, Domide, Perdikis, Triebkorn, Stefanovski, Pai, Prodan, Valean, Palmer, Langford, Blickensdörfer, van der Vlag, Diaz-Pier, Peyser, Woodman, Zehl, Fousek, Petkoski, Kusch, Hashemi, Marinazzo, Mangin, Flöel, Akintoye, Stahl, Deco, McIntosh, Hilgetag, Morgan, Schuller, Upton, McMurtrie, Dickscheid, Bjaalie, Amunts, Mersmann, Jirsa, Ritter (2022). Brain Simulation as a Cloud Service: The Virtual Brain on the European Research Platform EBRAINS. Neuroimage

• Sanz-Leon, P., Knock, S. A., Spiegler, A., & Jirsa, V. K. (2015). Mathematical framework for large-scale brain network modeling in The Virtual Brain. Neuroimage

What can I find here?

• Presentation slides from the course's lecture.
• The notebook (SimulateWithEBRAINS.zip) demonstrated during the workshop.

Guide to run the use-case notebook

1. Run the EBRAINS TVB-Multiscale app by browsing to 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!)
2. Navigate to "Contributed-Notebooks" folder, which offers user-specific persistent storage.
3. Upload and unzip there SimulateWithEBRAINS.zip by starting a terminal session or a new notebook and running unzip SimulateWithEBRAINS.zip
4. Run the TVB-corr-cortex-opt.ipynb notebook for TVB-ANNarchy cosimulation and the ANNarchy-spiking-cortex.ipynb one for ANNarchy only simulation.