Frontiers in Neuroinformatics (Nov 2015)

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

  • Henrik eMatzke,
  • Henrik eMatzke,
  • Henrik eMatzke,
  • Michael eSchirner,
  • Michael eSchirner,
  • Daniel eVollbrecht,
  • Daniel eVollbrecht,
  • Simon eRothmeier,
  • Simon eRothmeier,
  • Simon eRothmeier,
  • Adalberto eLlarena,
  • Adalberto eLlarena,
  • Adalberto eLlarena,
  • Raúl eRojas,
  • Paul eTriebkorn,
  • Lia eDomide,
  • Jochen eMersmann,
  • Viktor eJirsa,
  • Randy eMcIntosh,
  • Petra eRitter,
  • Petra eRitter,
  • Petra eRitter,
  • Petra eRitter

DOI
https://doi.org/10.3389/fninf.2015.00027
Journal volume & issue
Vol. 9

Abstract

Read online

The Virtual Brain (TVB; www.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 modelling 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 modelling; (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 modelling 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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