TVB-EduPack—An Interactive Learning and Scripting Platform for The Virtual Brain

The Virtual Brain (TVB; thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data. The framework addresses clinical and neuroscientific questions by simulating multi-scale neural dynamics that range from local population ac...

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Published in:Frontiers in neuroinformatics Vol. 9; p. 27
Main Authors: Matzke, Henrik, Schirner, Michael, Vollbrecht, Daniel, Rothmeier, Simon, Llarena, Adalberto, Rojas, Raúl, Triebkorn, Paul, Domide, Lia, Mersmann, Jochen, Solodkin, Ana, Jirsa, Viktor K., McIntosh, Anthony Randal, Ritter, Petra
Format: Journal Article
Language:English
Published: Switzerland Frontiers Research Foundation 25.11.2015
Frontiers Media S.A
Subjects:
Automation
Bioinformatics
Brain mapping
Brain Modelling
Brain research
Computational neuroscience
connectome
Educational Platform
EEG
Functional magnetic resonance imaging
Instructional design
Interactive learning
Mathematical problems
Medical imaging
Nervous system
Neural networks
Neuroimaging
Neuroscience
Neurosciences
NMR
Nuclear magnetic resonance
Open source software
Physiology
Population
the virtual brain
User interface
Germany
brain modeling
educational platform
connectome
computational neuroscience
The Virtual Brain
ISSN:1662-5196, 1662-5196
Online Access:Get full text
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Summary:The Virtual Brain (TVB; thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data. The framework addresses clinical and neuroscientific questions by simulating multi-scale neural dynamics that range from local population activity to large-scale brain function and related macroscopic signals like electroencephalography and functional magnetic resonance imaging. TVB is equipped with a graphical and a command-line interface to create models that capture the characteristic biological variability to predict the brain activity of individual subjects. To enable researchers from various backgrounds a quick start into TVB and brain network modeling in general, we developed an educational module: TVB-EduPack. EduPack offers two educational functionalities that seamlessly integrate into TVB's graphical user interface (GUI): (i) interactive tutorials introduce GUI elements, guide through the basic mechanics of software usage and develop complex use-case scenarios; animations, videos and textual descriptions transport essential principles of computational neuroscience and brain modeling; (ii) an automatic script generator records model parameters and produces input files for TVB's Python programming interface; thereby, simulation configurations can be exported as scripts that allow flexible customization of the modeling process and self-defined batch- and post-processing applications while benefitting from the full power of the Python language and its toolboxes. This article covers the implementation of TVB-EduPack and its integration into TVB architecture. Like TVB, EduPack is an open source community project that lives from the participation and contribution of its users. TVB-EduPack can be obtained as part of TVB from thevirtualbrain.org.
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Reviewed by: Marc De Kamps, University of Leeds, UK; Chung-Chuan Lo, National Tsing Hua University, Taiwan
These authors have contributed equally to this work.
Edited by: Arjen Van Ooyen, VU University Amsterdam, Netherlands
ISSN:1662-5196
1662-5196
DOI:10.3389/fninf.2015.00027