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

• 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
• DOI: 10.3389/fninf.2015.00027

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.