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

doi:10.1016/j.neuroimage.2022.118973

Brain simulation as a cloud service: The Virtual Brain on EBRAINS

Neuroimage. 2022 May 1:251:118973. doi: 10.1016/j.neuroimage.2022.118973. Epub 2022 Feb 4.

Authors

Michael Schirner¹, Lia Domide², Dionysios Perdikis³, Paul Triebkorn⁴, Leon Stefanovski³, Roopa Pai³, Paula Prodan², Bogdan Valean², Jessica Palmer³, Chloê Langford³, André Blickensdörfer³, Michiel van der Vlag⁵, Sandra Diaz-Pier⁵, Alexander Peyser⁵, Wouter Klijn⁵, Dirk Pleiter⁶, Anne Nahm⁷, Oliver Schmid⁸, Marmaduke Woodman⁹, Lyuba Zehl¹⁰, Jan Fousek⁹, Spase Petkoski⁹, Lionel Kusch⁹, Meysam Hashemi⁹, Daniele Marinazzo¹¹, Jean-François Mangin¹², Agnes Flöel¹³, Simisola Akintoye¹⁴, Bernd Carsten Stahl¹⁵, Michael Cepic¹⁶, Emily Johnson¹⁶, Gustavo Deco¹⁷, Anthony R McIntosh¹⁸, Claus C Hilgetag¹⁹, Marc Morgan⁸, Bernd Schuller⁷, Alex Upton²⁰, Colin McMurtrie²⁰, Timo Dickscheid¹⁰, Jan G Bjaalie²¹, Katrin Amunts²², Jochen Mersmann²³, Viktor Jirsa⁹, Petra Ritter²⁴

Affiliations

¹ 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. Electronic address: michael.schirner@bih-charite.de.
² Codemart, Str. Petofi Sandor, Cluj, Napoca, Romania.
³ 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.
⁴ 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.
⁵ SimLab Neuroscience, Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, JARA, Forschungszentrum Jülich GmbH, Jülich, Germany.
⁶ Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany; Institut für Theoretische Physik, Universität Regensburg, Regensburg, Germany.
⁷ Jülich Supercomputer Centre, Forschungszentrum Jülich, Jülich, Germany.
⁸ Swiss Federal Institute of Technology Lausanne (EPFL), Campus Biotech, Geneva, Switzerland.
⁹ Institut de Neurosciences des Systèmes, Aix Marseille Université, Marseille, France.
¹⁰ Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany.
¹¹ Department of Data-Analysis, Faculty of Psychology and Educational Sciences, Ghent University, Belgium; San Camillo IRCSS, Venice, Italy.
¹² Université Paris-Saclay, CEA, CNRS, Neurospin, Baobab, Gif-sur-Yvette, France.
¹³ Department of Neurology, University Medicine Greifswald, Greifswald, Germany; German Center for Neurodegenerative Diseases (DZNE) Standort Greifswald, Greifswald, Germany.
¹⁴ Leicester De Montfort Law School, De Montfort University, Leicester, United Kingdom.
¹⁵ Centre for Computing and Social Responsibility, De Montfort University, Leicester, United Kingdom.
¹⁶ Department of Innovation and Digitalisation in Law, Faculty of Law, University of Vienna, Austria.
¹⁷ 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.
¹⁸ Baycrest Health Sciences, Rotman Research Institute, Toronto, ON, Canada.
¹⁹ 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.
²⁰ CSCS Swiss National Supercomputing Centre, Lugano, Switzerland.
²¹ Institute of Basic Medical Sciences, University of Oslo, Norway.
²² 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.
²³ CodeBox GmbH, Stuttgart, Germany.
²⁴ 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. Electronic address: petra.ritter@bih-charite.de.

PMID: 35131433
DOI: 10.1016/j.neuroimage.2022.118973

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.

Keywords: Brain modelling; Cloud; Connectome; Data protection; High performance computing; Network model; Neuroimaging; Reproducibility.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bayes Theorem
Brain* / diagnostic imaging
Cloud Computing*
Computer Simulation
Humans
Magnetic Resonance Imaging / methods
Mice
Software