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Journal Article

TVB-EduPack: An interactive learning and scripting platform for The Virtual Brain

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Matzke,  Henrik
Minerva Research Group Brain Modes, MPI for Human Cognitive and Brain Sciences, Max Planck Society;
Department of Neurology, Charité University Medicine Berlin, Germany;
State Dependencies of Learning, Bernstein Center for Computational Neuroscience, Berlin, Germany;

Rothmeier,  Simon
Minerva Research Group Brain Modes, MPI for Human Cognitive and Brain Sciences, Max Planck Society;
Department of Neurology, Charité University Medicine Berlin, Germany;
State Dependencies of Learning, Bernstein Center for Computational Neuroscience, Berlin, Germany;

/persons/resource/persons37826

Ritter,  Petra
Minerva Research Group Brain Modes, MPI for Human Cognitive and Brain Sciences, Max Planck Society;
Department of Neurology, Charité University Medicine Berlin, Germany;
State Dependencies of Learning, Bernstein Center for Computational Neuroscience, Berlin, Germany;
Berlin School of Mind and Brain, Humboldt University Berlin, Germany;

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Citation

Matzke, H., Schirner, M., Vollbrecht, D., Rothmeier, S., Llarena, A., Rojas, R., et al. (2015). TVB-EduPack: An interactive learning and scripting platform for The Virtual Brain. Frontiers in Neuroinformatics, 9: 27. doi:10.3389/fninf.2015.00027.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0028-F29F-4
Abstract
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.