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

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.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-F29F-4 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-77B6-A
Genre: Journal Article

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 Creators:
Matzke, Henrik1, 2, 3, Author
Schirner, Michael2, 3, Author
Vollbrecht, Daniel2, 3, Author
Rothmeier, Simon1, 2, 3, Author
Llarena, Adalberto2, 3, 4, Author
Rojas, Raúl4, Author
Triebkorn, Paul2, Author
Domide, Lia5, Author
Mersmann, Jochen6, Author
Solodkin, Ana7, Author
Jirsa, Viktor K.8, Author
McIntosh, Anthony R.9, Author
Ritter, Petra1, 2, 3, 10, Author              
Affiliations:
1Minerva Research Group Brain Modes, MPI for Human Cognitive and Brain Sciences, Max Planck Society, ou_751546              
2Department of Neurology, Charité University Medicine Berlin, Germany, ou_persistent22              
3State Dependencies of Learning, Bernstein Center for Computational Neuroscience, Berlin, Germany, ou_persistent22              
4Intelligent Systems and Robotics Lab, Department of Mathematics and Computer Science, FU Berlin, Germany, ou_persistent22              
5Codemart, Cluj-Napoca, Romania, ou_persistent22              
6CodeBox GmbH, Stuttgart, Germany, ou_persistent22              
7Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, USA, ou_persistent22              
8Institut de Neurosciences des Systèmes, Aix-Marseille Université Faculté de Médecine, France, ou_persistent22              
9Rotman Research Institute, University of Toronto, ON, Canada, ou_persistent22              
10Berlin School of Mind and Brain, Humboldt University Berlin, Germany, ou_persistent22              

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Free keywords: The Virtual Brain; Brain modeling; Computational neuroscience; Connectome; Educational platform
 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.

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Language(s): eng - English
 Dates: 2015-06-092015-11-032015-11-25
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.3389/fninf.2015.00027
PMID: 26635597
PMC: PMC4658631
Other: eCollection 2015
 Degree: -

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Title: Frontiers in Neuroinformatics
  Abbreviation : Front Neuroinform
Source Genre: Journal
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Publ. Info: Lausanne, Switzerland : Frontiers Research Foundation
Pages: - Volume / Issue: 9 Sequence Number: 27 Start / End Page: - Identifier: ISSN: 1662-5196
CoNE: https://pure.mpg.de/cone/journals/resource/1662-5196