The Virtual Brain

Get up to speed about the fundamental principles of full brain network modeling using the open-source neuroinformatics platform The Virtual Brain (TVB).

TVB enables biologically realistic modeling of network dynamics using Connectome-based approaches across different brain scales.

Generate macroscopic neuroimaging signals including fMRI, intracranial and stereotactic EEG, surface EEG and MEG for single subjects.

Researchers from different backgrounds can benefit from an integrative software platform including a supporting framework for data management (generation, organization, storage, integration and sharing) and a simulation core written in Python.

The architecture of TVB supports interaction with MATLAB packages, e.g. the well-known Brain Connectivity Toolbox.

Simulated brains. Real memories.

After the workshop you should have a basic picture of how these models are built, how they work, and what biological properties of a neural system they represent. In addition, we will highlight several research topics that can be explored using this tool.

For the brave ones who like diving directly into the code, we expect you to know some Python, MATLAB, Octave, or whatever programming language you like the most.

The workshop is organized with interleaved oral presentation and hands-on sessions. Attendants will have the time to ask questions.

The hands-on sessions will let you immediately apply the concepts from the lectures to your simulations in TVB.

Combine your visit with BCW & OHBM 2014

TVB#Node1 will take place back to back with two important neuroscience conferences, also in Hamburg, Germany:

• Brain Connectivity Workshop 2014
• 2014 meeting of the Organization for Human Brain Mapping

Scientists from the TVB team are already confirmed speakers for various sessions there.

Prepare your gear

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:

• Download and install the latest stable TVB package.
• Test it in its current form to make sure it's compatible with your computing environment.
• Familiarize yourself with the basics by browsing through the included manual (TVB-Distribution/docs/UserManual.pdf).

Meet the TVB team

Apart from learning together, you can meet and talk to a good part of The Virtual Brain's core team, covering a broad range of topics from cutting-edge neuroscience research to advanced software development.

• Tanya Brown, Toronto
• Michael Burgstahler, Stuttgart
• Lia Domide, Cluj-Napoca
• Mathieu Golos, Marseille
• Viktor Jirsa, Marseille
• Randy McIntosh, Toronto
• Jochen Mersmann, Stuttgart
• Tim Proix, Marseille
• Petra Ritter, Berlin
• Paula Sanz-Leon, Marseille
• Ana Solodkin, San Diego
• Marmaduke Woodman, Marseille

Program: Morning Session

• 09:00 - 09:15 am

  Can I please get a coffee first?

  A caffeinated history of The Virtual Brain

• 09:15 - 10:00 am

  A generative model of the brain: Describing the building blocks of a brain network model

  Learn about the basic principles and assumptions underlying a brain network model, recent studies using different local models, cortical connectivity and dynamical units. Understand how to approximate neural fields.

• 10:00 - 10:30 am

  Interacting with TVB

  Follow the presenters with your own laptop, learning about the web UI as well as the command line and scripting interfaces using Python and MatLab.

• 10:30 - 11:00 am

  Coffee break

• 11:00 - 11:30 am

  How to obtain a TVB friendly dataset

  Understand how a complete TVB dataset works, which neuroimaging data formats can be imported and how to set up data-obtaining pipelines extracting subject-specific structural data.

• 11:30 - 12:30 am

  Hands-on: Build your own brain network

  Follow the presenters and build your own model, running a host of simulations against it: region-based, local dynamics, parameter space exploration, obtaining functional data like fMRI or EEG, differential simulation analysis with and without noise, surface-based and local connectivity structures

• 12:30 - 02:00 pm

  Lunch break

Program: Afternoon Session

• 02:00 - 02:20 pm

  Exporting and sharing your TVB data & results

  See how you can export your results from TVB to do more specific analyses in other computing environments.

• 02:20 - 02:50 pm

  Using TVB to determine functional mechanisms in chronic stroke

  See practical applications of TVB when studying the effects of chronic strokes.

• 02:50 - 03:20 pm

  Hands-on: Modeling the impact of structural lesions

  Follow the design of a simulation protocol where the Connectome is the "parameter" to be explored. Learn about the effects of conduction speed and time delays to reveal the space-time structure of the connectivity matrix.

• 03:20 - 03:40 pm

  Hands-on: Beyond resting-state and homogeneous models

  Design stimuli to simulate task-driven activity. Use parameter dispersion or spatialization by assigning different dynamical regimes to every node.

• 03:40 - 04:10 pm

  Coffee break

• 04:10 - 04:40 pm

  The epileptic brain: Introducing the Epileptor

  Learn about a specific local model that explains the nature of seizure dynamics.

• 04:40 - 05:10 pm

  Hands-on: Modeling epilepsy using TVB

  Build a working example of an epileptic brain on your own laptop.

• Closing remarks