The Virtual Brain

4 DAY WORKSHOP :: MARCH 9-12, 2020

The TVB Berlin team is organizing TVB Node #10: Personalized Multi-Scale Brain Simulation on March 9-12, 2020, in Berlin.

This new Node workshop is also an official elective course of the Bernstein Center for Computational Neuroscience Berlin.

This course provides basic knowledge on personalized brain network modeling. Required interdisciplinary methods will be introduced. A focus will be set on the open-source simulation platform The Virtual Brain (TVB), and basic concepts and methods will be introduced. Participants will gain theoretical knowledge and subsequently, use this knowledge to construct brain models, process multimodal neuroimaging data for creating individual brain, run simulations and use supporting neuroinformatics tools such as collaboratories, pipelines, workflows and data repositories. Participants will be able to operate the open-source neuroinformatics platform TVB. The following topics will be covered:

• Theoretical background of large-scale brain network model and concepts of nonlinear dynamics (bifurcation analysis, phase plane, flows on manifolds)
  

• Architecture of TVB simulator
  

• Interacting with TVB using GUI and CLI
  

• Modeling resting-state networks activity in human, mouse, and macaque brain
  

• Parameter optimization and model inference
  

• Visualization of multimodal brain dynamics
  

• Application of brain network modeling for clinical questions such as in epilepsy

• Multiscale co-simulation using TVB and microscopic simulators such as NEST

• Personalization pipelines: processing of brain images (MRI, fMRI, DTI, PET) and electrophysiological data (EEG, MEG) for individualization of brain network model
  

• Running workflows on high performance computers
  

• Making use of and contributing to collaborative informatics simulation platforms such as Human Brain Project’s EBRAINS
  

Preliminary Program

The workshop consists of 4 full-day sessions:

March 9, Conference Room 1

• 09:00 - 10:30

  Introduction to The Virtual Brain (TVB) simulation platform (Lecture)
  

• 10:30 - 11:30

  Architecture of TVB (Lecture)
  

• 11:30 - 13:00

  Neural population models in TVB and Phase Plane Viewer (Lecture)
  

• 13:00 - 14:00
  

  Lunch break
  

• 14:00 - 15:00

  Import TVB ready data to TVB and create a brain model (Tutorial)
  

• 15:00 - 16:00

  My first simulation (Tutorial)
  

• 16:00 - 18:00

  The Virtual Mouse Brain (TVMB): Simulate a mouse brain network model (Tutorial)
  

March 10, Conference Room 1

• 09:00 - 10:00

  Bridging multiscale in TVB (Lecture)
  

• 10:00 - 12:00

  Perform a multiscale co-simulation with TVB-NEST (Tutorial)

• 12:00 - 13:00

  Generate a macaque brain model (Tutorial)

• 13:00 - 14:00
  

  Lunch break
  

• 14:00 - 16:00
  

  Introduction to surface-based simulation modeling (Lecture)
  

• 16:00 - 18:00
  

  Perform a surface-based simulation (Tutorial)
  

March 11, Conference Room 1

• 09:00 - 11:30
  

  Generating TVB ready imaging data (Lecture)
  

• 11:30 - 13:00
  

  Operating pipelines on High Performance Computers (Lecture)
  

• 13:00 - 14:00
  

  Lunch break
  

• 14:00 - 16:00
  

  Generate your own 3D Brain model outside TVB (Tutorial)
  

• 16:00 - 18:00
  

  Simulate a Virtual Epileptic Patient (Tutorial)
  

March 12, Conference Room 1

• 09:00 - 10:30
  

  Parameter optimization (Lecture)
  

• 10:30 - 12:00
  

  Introduction to birfurcation theory and analyses (Lecture)
  

• 12:00 - 13:00
  

  Visualization of a bifurcation diagram: example with the Jansen Rit model (Lecture)
  

• 13:00 - 14:00
  

  Lunch break
  

• 14:00 - 16:00
  

  My first bifurcation diagram (Tutorial)
  

• 16:00 - 18:00
  

  Wrap-up and assignments

Location

The workshop will be held at the Brain Simulation Section, of the Charité - University Medicine Berlin, which is located at CCM-Luisen-Carreé.

Registration

Registration to The Virtual Brain workshop is required for attending the workshop. Anyone is welcome to register for TVB Node #10! You DO NOT need to be registered as a student at BCCN Berlin in order to participate in this workshop.

To register, please send an email to Julie Courtiol julie.courtiol@charite.de. Make sure to register early as we only offer limited seats to ensure there are enough tutors for you.

2 ECTS are awarded to BCCN students upon successful completion of the course.

IMPORTANT DETAILS

Equipment. Please bring your own laptop to work on, and follow the steps below to prepare your software environment.

Prepare for the workshop

To get the most out of this workshop as an attendee, you might want to get a head-start by preparing your gear before you arrive:

1. Download and install the latest stable TVB package,
   
2. Test it in its current form to make sure it’s compatible with your computing environment,
   
3. Familiarize yourself with the basics by browsing through the included manual (once downloaded TVB, located at /TVB-Distribution/docs/UserManual.pdf),
   
4. If you are interested in modifying the code and contributing to TVB, also install the version control system Git.
   

In case of any technical problems with TVB installation, please head over to the TVB mailing list.