NeuroImage (May 2022)
Brain simulation as a cloud service: The Virtual Brain on EBRAINS
- Michael Schirner,
- Lia Domide,
- Dionysios Perdikis,
- Paul Triebkorn,
- Leon Stefanovski,
- Roopa Pai,
- Paula Prodan,
- Bogdan Valean,
- Jessica Palmer,
- Chloê Langford,
- André Blickensdörfer,
- Michiel van der Vlag,
- Sandra Diaz-Pier,
- Alexander Peyser,
- Wouter Klijn,
- Dirk Pleiter,
- Anne Nahm,
- Oliver Schmid,
- Marmaduke Woodman,
- Lyuba Zehl,
- Jan Fousek,
- Spase Petkoski,
- Lionel Kusch,
- Meysam Hashemi,
- Daniele Marinazzo,
- Jean-François Mangin,
- Agnes Flöel,
- Simisola Akintoye,
- Bernd Carsten Stahl,
- Michael Cepic,
- Emily Johnson,
- Gustavo Deco,
- Anthony R. McIntosh,
- Claus C. Hilgetag,
- Marc Morgan,
- Bernd Schuller,
- Alex Upton,
- Colin McMurtrie,
- Timo Dickscheid,
- Jan G. Bjaalie,
- Katrin Amunts,
- Jochen Mersmann,
- Viktor Jirsa,
- Petra Ritter
Affiliations
- Michael Schirner
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany; Bernstein Focus State Dependencies of Learning & Bernstein Center for Computational Neuroscience Berlin, Germany; Einstein Center for Neuroscience Berlin, Charitéplatz 1, 10117 Berlin, Germany; Einstein Center Digital Future, Wilhelmstraße 67, 10117 Berlin, Germany; Corresponding authors.
- Lia Domide
- Codemart, Str. Petofi Sandor, Cluj, Napoca, Romania
- Dionysios Perdikis
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany
- Paul Triebkorn
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany; Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France
- Leon Stefanovski
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany
- Roopa Pai
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany
- Paula Prodan
- Codemart, Str. Petofi Sandor, Cluj, Napoca, Romania
- Bogdan Valean
- Codemart, Str. Petofi Sandor, Cluj, Napoca, Romania
- Jessica Palmer
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany
- Chloê Langford
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany
- André Blickensdörfer
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany
- Michiel van der Vlag
- SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
- Sandra Diaz-Pier
- SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
- Alexander Peyser
- SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
- Wouter Klijn
- SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany
- Dirk Pleiter
- Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany; Institut für Theoretische Physik, Universität Regensburg, Regensburg, Germany
- Anne Nahm
- Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany
- Oliver Schmid
- Swiss Federal Institute of Technology Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
- Marmaduke Woodman
- Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France
- Lyuba Zehl
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Jan Fousek
- Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France
- Spase Petkoski
- Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France
- Lionel Kusch
- Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France
- Meysam Hashemi
- Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France
- Daniele Marinazzo
- Department of Data-Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Belgium; San Camillo IRCSS, Venice, Italy
- Jean-François Mangin
- Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab, Gif-sur-Yvette, France
- Agnes Flöel
- Department of Neurology, University Medicine Greifswald, Greifswald, Germany; German Center for Neurodegenerative Diseases (DZNE) Standort Greifswald, Greifswald, Germany
- Simisola Akintoye
- Leicester De Montfort Law School, De Montfort University, Leicester, United Kingdom
- Bernd Carsten Stahl
- Centre for Computing and Social Responsibility, De Montfort University, Leicester, United Kingdom
- Michael Cepic
- Department of Innovation and Digitalisation in Law, Faculty of Law, University of Vienna, Austria
- Emily Johnson
- Department of Innovation and Digitalisation in Law, Faculty of Law, University of Vienna, Austria
- Gustavo Deco
- Center for Brain and Cognition, Computational Neuroscience Group, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain; Institució Catalana de la Recerca i Estudis Avançats, Barcelona, Spain; Department of Neuropsychology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; School of Psychological Sciences, Turner Institute for Brain and Mental Health, Monash University, Melbourne, Clayton, Australia
- Anthony R. McIntosh
- Baycrest Health Sciences, Rotman Research Institute, Toronto, ON, Canada
- Claus C. Hilgetag
- Institute of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Health Sciences, Boston University, 635 Commonwealth Ave., Boston, Massachusetts 02215, United States
- Marc Morgan
- Swiss Federal Institute of Technology Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
- Bernd Schuller
- Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany
- Alex Upton
- CSCS Swiss National Supercomputing Centre, Lugano, Switzerland
- Colin McMurtrie
- CSCS Swiss National Supercomputing Centre, Lugano, Switzerland
- Timo Dickscheid
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Jan G. Bjaalie
- Institute of Basic Medical Sciences, University of Oslo, Norway
- Katrin Amunts
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany; C. and O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Germany
- Jochen Mersmann
- CodeBox GmbH, Stuttgart, Germany
- Viktor Jirsa
- Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France
- Petra Ritter
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Department of Neurology with Experimental Neurology, Charitéplatz 1, 10117 Berlin, Germany; Bernstein Focus State Dependencies of Learning & Bernstein Center for Computational Neuroscience Berlin, Germany; Einstein Center for Neuroscience Berlin, Charitéplatz 1, 10117 Berlin, Germany; Einstein Center Digital Future, Wilhelmstraße 67, 10117 Berlin, Germany; Corresponding authors.
- Journal volume & issue
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Vol. 251
p. 118973
Abstract
The Virtual Brain (TVB) is now available as open-source services on the cloud research platform EBRAINS (ebrains.eu). It offers software for constructing, simulating and analysing brain network models including the TVB simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional brain networks; combined simulation of large-scale brain networks with small-scale spiking networks; automatic conversion of user-specified model equations into fast simulation code; simulation-ready brain models of patients and healthy volunteers; Bayesian parameter optimization in epilepsy patient models; data and software for mouse brain simulation; and extensive educational material. TVB cloud services facilitate reproducible online collaboration and discovery of data assets, models, and software embedded in scalable and secure workflows, a precondition for research on large cohort data sets, better generalizability, and clinical translation.
