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

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 ac...

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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
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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.
AbstractList	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.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. 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. 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.
Author	Jirsa, Viktor K. McIntosh, Anthony Randal Mersmann, Jochen Matzke, Henrik Ritter, Petra Domide, Lia Vollbrecht, Daniel Schirner, Michael Triebkorn, Paul Rojas, Raúl Solodkin, Ana Rothmeier, Simon Llarena, Adalberto
AuthorAffiliation	3 Bernstein Focus State Dependencies of Learning and Bernstein Center for Computational Neuroscience Berlin, Germany 9 Rotman Research Institute of Baycrest Centre, University of Toronto Toronto, ON, Canada 1 Minerva Research Group BrainModes, Max Planck Institute for Human Cognitive and Brain Sciences Leipzig, Germany 5 Codemart Cluj-Napoca, Romania 6 CodeBox GmbH Stuttgart, Germany 10 Berlin School of Mind and Brain and Mind and Brain Institute, Humboldt University Berlin, Germany 2 Department of Neurology, Charité – University Medicine Berlin, Germany 4 Intelligent Systems and Robotics Lab, Department of Mathematics and Computer Science, Free University Berlin, Germany 8 Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes UMR 1106, Université d'Aix-Marseille Marseille, France 7 Departments of Anatomy & Neurobiology and Neurology, School of Medicine, University of California, Irvine Irvine, CA, USA
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Keywords	brain modeling educational platform connectome computational neuroscience The Virtual Brain
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Reviewed by: Marc De Kamps, University of Leeds, UK; Chung-Chuan Lo, National Tsing Hua University, Taiwan These authors have contributed equally to this work. Edited by: Arjen Van Ooyen, VU University Amsterdam, Netherlands
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Snippet	The Virtual Brain (TVB; thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data.... The Virtual Brain (TVB; www.thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity...
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SubjectTerms	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
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Title	TVB-EduPack—An Interactive Learning and Scripting Platform for The Virtual Brain
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