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

Daniel Vollbrecht1, 2, Henrik Matzke1, 2, 3, Michael Schirner1, 2, Simon Rothmeier1, 2, 3, Adalberto Llarena1, 2, 4, Paul Triebkorn1, Lia Domide5, Jochen Mersmann6, Viktor K. Jirsa7, Anthony R. McIntosh8 and Petra Ritter1, 2, 3, 9*
  • 1 Charité – University Medicine Berlin, Dept. Neurology, Germany
  • 2 Bernstein Focus State Dependencies of Learning & Bernstein Center for Computational Neuroscience Berlin, Germany
  • 3 Minerva Research Group BrainModes, Max Planck Institute for Human Cognitive and Brain Sciences Leipzig, Germany
  • 4 Freie Universität Berlin, Department of Mathematics and Computer Science, Germany
  • 5 Codemart, Romania
  • 6 CodeBox GmbH, Germany
  • 7 Aix-Marseille Université Faculté de Médecine, Institut de Neurosciences des Systèmes UMR INSERM 1106, France
  • 8 University of Toronto, Rotman Research Institute of Baycrest Centre, Canada
  • 9 Humboldt University of Berlin, Berlin School of Mind and Brain & Mind and Brain Institute, Germany

The Virtual Brain (TVB; thevirtualbrain.org) is a neuroinformatics platform for full brain network simulation based on individual anatomical connectivity data. In order to ease familiarization and to enable users to quickly start working with TVB, we developed our newly released educational module: TVB-EduPack (Matzke, Schirner, 2015; in prep.) provides researchers from various backgrounds a quick start into TVB and brain network modelling. The possibility to create extendable educational content that is supported by animations, videos and textual descriptions addresses the demand for a flexible educational framework which can easily provide user group fitted interactive tutorials. In contrast to standard documentation, TVB-EduPack tutorials allow users to directly engage in complex modelling scenarios while using TVB. The educational component of TVB-EduPack comprises two different knowledge levels: (i) EduStart, an interactive introduction into the software TVB that makes the user familiar with the basic usability while guiding through concepts and methodologies in computational neuroscience and (ii) EduCase, which refers to advanced use cases in TVB, e.g. developing computational neuroscience methods further by leading the user through in-depth tutorials that exemplify typical applications like exploring dynamical regimes of different models or tuning parameters to reproduce specific types of neuronal activity. We show several use cases and demonstrate how autodidactic exercising of complex TVB simulation scenarios creates a pleasant user experience. Additionally, TVB-EduPack contains a graphical script creation tool that records GUI interactions and thereby allows users to create re-usable and modifiable batch scripts for the TVB console interface in order to automate or demonstrate their work. Like TVB, EduPack is an open source community project that lives from the participation and contribution of its users.

Acknowledgements

The authors acknowledge the support of the James S. McDonnell Foundation (Brain Network Recovery Group JSMF22002082), the German Ministry of Education and Research (Bernstein Focus State Dependencies of Learning 01GQ0971) and the Max-Planck Society (Minerva Program).

References

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Matzke, H. (2014). TVB-EduPack - An interactive learning and scripting platform for The Virtual Brain, Master's thesis, Free University Berlin.
Ritter, P., M. Schirner, A. R. McIntosh and V. K. Jirsa (2013). "The virtual brain integrates computational modeling and multimodal neuroimaging." Brain connectivity 3(2): 121-145.
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Schirner, M., S. Rothmeier, V. K. Jirsa, A. R. McIntosh and P. Ritter (2015). "Constructing subject-specific virtual brains from multimodal neuroimaging data." Neuroimage - Under Review NIMG-14-2505.
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Keywords: the virtual brain, connectome, full-brain network model, virtual brain, large-scale simulation, web platform, Brain Modelling, Educational framework, Interactive tutorial, community project, Interactive Learning, python, JavaScript, DOM model, XML, open source, Educational Platform

Conference: Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.

Presentation Type: Demo, to be considered for oral presentation

Topic: General neuroinformatics

Citation: Vollbrecht D, Matzke H, Schirner M, Rothmeier S, Llarena A, Triebkorn P, Domide L, Mersmann J, Jirsa VK, McIntosh AR and Ritter P (2015). TVB-EduPack – An interactive learning and scripting platform for The Virtual Brain. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00046

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Received: 31 May 2015; Published Online: 05 Aug 2015.

* Correspondence: Dr. Petra Ritter, Minerva Research Group BrainModes, Max Planck Institute for Human Cognitive and Brain Sciences Leipzig, Berlin, 10117, Germany, petra.ritter@charite.de