The Virtual Brain

2 DAY WORKSHOP :: AUGUST 7-8, 2018

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

TVB NODE#7 is an official satellite event to
Neuroinformatics 2018.
Be sure to register for both!

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.

Personalized brain network models can be derived from an individual’s MRI data.

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. Applications to use cases in the healthy and diseased brain are explicitly presented.

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.

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.

Refreshments will be available during the breaks and lunch will be provided.

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).
• 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, head over to the TVB user forum on Google Groups

Meet the TVB team

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

Program: DAY 1

• 08:30 - 09:00

  Arrival, registration & coffee

• 09:00 - 09:15

  Introduction to Node 7 workshop
  

• 09:15 - 10:45

  A generative model of the brain
  Describing the building blocks of a brain network model basic principles and assumptions, recent studies with different local models approximation of neural fields
  RANDY MCINTOSH
  

• 10:45 - 11:00

  Coffee Break
  

• 11:00 - 11:45

  Architecture of TVB
  Overview of the software architecture of The Virtual Brain
  PAULA POPA - CODEMART
  MIHAI ANDREAI - CODEMART
  

• 11:45 - 12:30

  Hands-On:: Interacting with TVB using GUI
  Learn to prepare and run TVB simulations through web interface
  PAUL TRIEBKORN - CHARITE, BERLIN

• 12:30 - 13:30

  Lunch break
  Lunch will be provided
  

• 13:30 - 14:15

  Use Case: Interacting with TVB using CLI
  Introduction to the Python interface of TVB
  PAUL TRIEBKORN - CHARITE, BERLIN

• 14:15 - 15:00

  Data fitting: theoretical background
  Fitting the model outputs and the measurements: parameter sweeps, Bayesian inference
  JOHN GRIFFITHS - BAYCREST, TORONTO
  

• 15:00 - 15:15

  Coffee break

• 15:15 - 16:00

  Modeling brain stimulation and mouse brains
  Modeling brain stimulation and exploring their dynamics
  ANDREAS SPIEGLER - CHARITE, BERLIN
  

• 16:00 - 16:45

  Hands-On: Modeling brain stimulation
  How to simulate brain stimulation
  PAUL TRIEBKORN - CHARITE, BERLIN
  

• 16:45 - 17:30

  Hands-On: Modeling mouse brains
  How to simulate mouse brains
  PAUL TRIEBKORN - CHARITE, BERLIN
  

• 17:30 - 18:00

  Recap & open discussion
  

Program: DAY 2

• 09:00 - 09:15
  Morning caffeine
  

• 9:15 - 10:00
  From imaging data to TVB datasets: conceptual introduction
  Overview of neuroimaging data formats, software, & steps to get TVB-compatible datasets
  PETRA RITTER - CHARITE, BERLIN
  

• 10:00 - 10:45
  From imaging data to TVB datasets
  Practical example of processing the neuroimaging data and import to TVB
  PETRA RITTER - CHARITE, BERLIN
  

• 10:45 - 11:00
  Coffee break
  

• 11:00 - 11:45
  Designing Clinical Research with TVB
  Case studies in Stroke and Alzheimer’s Disease
  ANA SOLODKIN - IRVINE, CA
  

• 11:45 - 12:30
  Hands-On: Modeling stroke
  Modeling stroke
  JOHN GRIFFITHS - BAYCREST, TORONTO
  ANA SOLODKIN - IRVINE, CA
  

• 12:30 - 13:30
  Lunch break
  

• 13:30 - 14:15
  Using TVB for epilepsy
  Examples clinical applications of TVB
  JULIE COURTIOL - CHARITE, BERLIN
  

• 14:15 - 15:00
  Hands-On: Modeling epilepsy
  Simulating epilepsy
  PAUL TRIEBKORN - CHARITE, BERLIN
  

• 15:00 - 15:15
  Coffee break
  

• 15:15 - 16:00
  Using TVB for neurodegenerative diseases
  Examples clinical applications of TVB
  ANA SOLODKIN - IRVINE, CA
  

• 16:00 - 17:00
  Hands-On: Modifying TVB code and implementing new features
  A guide on how to add new neural mass model, integration scheme, or a monitor to TVB
  JULIE COURTIOL - CHARITE, BERLIN
  

• 17:00 - 17:30
  Final discussion & closing remarks