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.
Highlights
The Virtual Brain (TVB; thevirtualbrain.org) is a Python-based neuroinformatics platform for the simulation of realistic largescale networks (Jirsa et al, 2010) of neural population models available for all major operating systems, including Windows, Mac OS, and Linux (Ritter et al, 2013; Sanz-Leon et al, 2013; Roy et al, 2014; Woodman et al, 2014)
Interactive tutorials guide the user in a step-by-step manner through use case examples that show how to perform advanced modeling with TVB. Using this instructional design framework, TVB-EduPack combines didactic preparations of computational neuroscience contents with practical results delivered by brain simulation
While earlier articles on TVB focused on the description of the mathematical framework, the software infrastructure and analyses of dynamics of brain network models, here we introduce an educational add-on module for TVB that enables new users to quickly familiarize themselves with TVB usage and brain network modeling in general
Summary
The Virtual Brain (TVB; thevirtualbrain.org) is a Python-based neuroinformatics platform for the simulation of realistic largescale networks (Jirsa et al, 2010) of neural population models available for all major operating systems, including Windows, Mac OS, and Linux (Ritter et al, 2013; Sanz-Leon et al, 2013; Roy et al, 2014; Woodman et al, 2014). TVB provides a generic framework for computational modeling and tools to extract structural and functional connectomes from multimodal datasets (Schirner et al, 2015) in order to link personalized brain network structure with neural population models It is an open-source whole-brain simulation platform that integrates empirical data of different modalities and spatial scales to construct comprehensive and biologically plausible models of global brain network dynamics. Using this instructional design framework, TVB-EduPack combines didactic preparations of computational neuroscience contents with practical results delivered by brain simulation. As modeling scenarios get more complex, users often switch to the programming interface To ease this transition, EduPack contains a script generation tool that automatically exports simulation script templates with model parameter and simulator configuration settings specified within the GUI. While earlier articles on TVB focused on the description of the mathematical framework, the software infrastructure and analyses of dynamics of brain network models, here we introduce an educational add-on module for TVB that enables new users to quickly familiarize themselves with TVB usage and brain network modeling in general
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