The Virtual Brain: a simulator of primate brain network dynamics

We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of m...

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Published in:Frontiers in neuroinformatics Vol. 7; p. 10
Main Authors: Sanz Leon, Paula, Knock, Stuart A., Woodman, M. Marmaduke, Domide, Lia, Mersmann, Jochen, McIntosh, Anthony R., Jirsa, Viktor
Format: Journal Article
Language:English
Published: Switzerland Frontiers Research Foundation 01.01.2013
Frontiers Media S.A
Subjects:
Bioinformatics
Brain mapping
Brain research
Computer programs
connectivity
connectome
EEG
Electroencephalography
Functional magnetic resonance imaging
Nervous system
neural field
neural mass
Neural networks
Neuroimaging
Neuroscience
python
Symmetry
virtual brain
Germany
python
large-scale simulation
connectome
web platform
full-brain network model
time delays
neural masses
virtual brain
ISSN:1662-5196, 1662-5196
Online Access:Get full text
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Summary:We present The Virtual Brain (TVB), a neuroinformatics platform for full brain network simulations using biologically realistic connectivity. This simulation environment enables the model-based inference of neurophysiological mechanisms across different brain scales that underlie the generation of macroscopic neuroimaging signals including functional MRI (fMRI), EEG and MEG. 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. TVB allows the reproduction and evaluation of personalized configurations of the brain by using individual subject data. This personalization facilitates an exploration of the consequences of pathological changes in the system, permitting to investigate potential ways to counteract such unfavorable processes. The architecture of TVB supports interaction with MATLAB packages, for example, the well known Brain Connectivity Toolbox. TVB can be used in a client-server configuration, such that it can be remotely accessed through the Internet thanks to its web-based HTML5, JS, and WebGL graphical user interface. TVB is also accessible as a standalone cross-platform Python library and application, and users can interact with the scientific core through the scripting interface IDLE, enabling easy modeling, development and debugging of the scientific kernel. This second interface makes TVB extensible by combining it with other libraries and modules developed by the Python scientific community. In this article, we describe the theoretical background and foundations that led to the development of TVB, the architecture and features of its major software components as well as potential neuroscience applications.
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Reviewed by: Ingo Bojak, University of Reading, UK; Hans Ekkehard Plesser, Norwegian University of Life Sciences, Norway; Laurent U. Perrinet, Centre National de la Recherche Scientifique, France
Edited by: Daniele Marinazzo, University of Gent, Belgium
ISSN:1662-5196
1662-5196
DOI:10.3389/fninf.2013.00010