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

Michael Schirner; Lia Domide; Dionysios Perdikis; Paul Triebkorn; Leon Stefanovski; Roopa Pai; Paula Popa; 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; Jochen Mersmann; Viktor Jirsa; Petra Ritter

doi:10.1016/j.neuroimage.2022.118973

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

Michael Schirner (Korresp. Autor*in)
, Lia Domide
, Dionysios Perdikis
, Paul Triebkorn
, Leon Stefanovski
, Roopa Pai
, Paula Popa
, 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, Jochen Mersmann, Viktor Jirsa, Petra Ritter

Institut für Innovation und Digitalisierung im Recht

Veröffentlichungen: Beitrag in Fachzeitschrift › Artikel › Peer Reviewed

Abstract

The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science. It offers services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional connectomes; multiscale co-simulation of spiking and large-scale networks; a domain specific language for automatic high-performance code generation from user-specified models; simulation-ready BNMs of patients and healthy volunteers; Bayesian inference of epilepsy spread; data and code 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.

Originalsprache	Englisch
Aufsatznummer	118973
Seitenumfang	11
Fachzeitschrift	NeuroImage
Jahrgang	251
DOIs	https://doi.org/10.1016/j.neuroimage.2022.118973
Publikationsstatus	Veröffentlicht - 1 Mai 2022

ÖFOS 2012

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10.1016/j.neuroimage.2022.118973Lizenz: CC BY 4.0

https://phaidra.univie.ac.at/o:1654579Lizenz: CC BY 4.0

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Zitationsweisen

Schirner, M., Domide, L., Perdikis, D., Triebkorn, P., Stefanovski, L., Pai, R., Popa, P., Valean, B., Palmer, J., Langford, C., Blickensdörfer, A., Vlag, M. V. D., Diaz-Pier, S., Peyser, A., Klijn, W., Pleiter, D., Nahm, A., Schmid, O., Woodman, M., ... Ritter, P. (2022). Brain simulation as a cloud service: The Virtual Brain on EBRAINS. NeuroImage, 251, Artikel 118973. https://doi.org/10.1016/j.neuroimage.2022.118973

@article{2cab78bc201941a6a8297107398fb09d,

title = "Brain simulation as a cloud service: The Virtual Brain on EBRAINS",

abstract = " The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science. It offers services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional connectomes; multiscale co-simulation of spiking and large-scale networks; a domain specific language for automatic high-performance code generation from user-specified models; simulation-ready BNMs of patients and healthy volunteers; Bayesian inference of epilepsy spread; data and code 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 = "cs.CE, cs.CR, cs.DC, q-bio.NC, q-bio.QM, Neuroimaging, Data protection, Brain modelling, Connectome, REPRODUCIBILITY, ATLAS, SPACE, CONNECTOME, High performance computing, Network model, Reproducibility, Cloud",

author = "Michael Schirner and Lia Domide and Dionysios Perdikis and Paul Triebkorn and Leon Stefanovski and Roopa Pai and Paula Popa and Bogdan Valean and Jessica Palmer and Chlo{\^e} Langford and Andr{\'e} Blickensd{\"o}rfer and Vlag, \{Michiel van der\} and Sandra Diaz-Pier and Alexander Peyser and Wouter Klijn and Dirk Pleiter and Anne Nahm and Oliver Schmid and Marmaduke Woodman and Lyuba Zehl and Jan Fousek and Spase Petkoski and Lionel Kusch and Meysam Hashemi and Daniele Marinazzo and Jean-Fran{\c c}ois Mangin and Agnes Fl{\"o}el and Simisola Akintoye and Stahl, \{Bernd Carsten\} and Michael Cepic and Emily Johnson and Gustavo Deco and McIntosh, \{Anthony R.\} and Hilgetag, \{Claus C.\} and Marc Morgan and Bernd Schuller and Alex Upton and Colin McMurtrie and Timo Dickscheid and Bjaalie, \{Jan G.\} and Jochen Mersmann and Viktor Jirsa and Petra Ritter",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s)",

year = "2022",

month = may,

day = "1",

doi = "10.1016/j.neuroimage.2022.118973",

language = "English",

volume = "251",

journal = "NeuroImage",

issn = "1053-8119",

publisher = "ACADEMIC PRESS INC ELSEVIER SCIENCE",

}

Schirner, M, Domide, L, Perdikis, D, Triebkorn, P, Stefanovski, L, Pai, R, Popa, P, Valean, B, Palmer, J, Langford, C, Blickensdörfer, A, Vlag, MVD, Diaz-Pier, S, Peyser, A, Klijn, W, Pleiter, D, Nahm, A, Schmid, O, Woodman, M, Zehl, L, Fousek, J, Petkoski, S, Kusch, L, Hashemi, M, Marinazzo, D, Mangin, J-F, Flöel, A, Akintoye, S, Stahl, BC, Cepic, M, Johnson, E, Deco, G, McIntosh, AR, Hilgetag, CC, Morgan, M, Schuller, B, Upton, A, McMurtrie, C, Dickscheid, T, Bjaalie, JG, Mersmann, J, Jirsa, V & Ritter, P 2022, 'Brain simulation as a cloud service: The Virtual Brain on EBRAINS', NeuroImage, Jg. 251, 118973. https://doi.org/10.1016/j.neuroimage.2022.118973

TY - JOUR

T1 - Brain simulation as a cloud service

T2 - The Virtual Brain on EBRAINS

AU - Schirner, Michael

AU - Domide, Lia

AU - Perdikis, Dionysios

AU - Triebkorn, Paul

AU - Stefanovski, Leon

AU - Pai, Roopa

AU - Popa, Paula

AU - Valean, Bogdan

AU - Palmer, Jessica

AU - Langford, Chloê

AU - Blickensdörfer, André

AU - Vlag, Michiel van der

AU - Diaz-Pier, Sandra

AU - Peyser, Alexander

AU - Klijn, Wouter

AU - Pleiter, Dirk

AU - Nahm, Anne

AU - Schmid, Oliver

AU - Woodman, Marmaduke

AU - Zehl, Lyuba

AU - Fousek, Jan

AU - Petkoski, Spase

AU - Kusch, Lionel

AU - Hashemi, Meysam

AU - Marinazzo, Daniele

AU - Mangin, Jean-François

AU - Flöel, Agnes

AU - Akintoye, Simisola

AU - Stahl, Bernd Carsten

AU - Cepic, Michael

AU - Johnson, Emily

AU - Deco, Gustavo

AU - McIntosh, Anthony R.

AU - Hilgetag, Claus C.

AU - Morgan, Marc

AU - Schuller, Bernd

AU - Upton, Alex

AU - McMurtrie, Colin

AU - Dickscheid, Timo

AU - Bjaalie, Jan G.

AU - Mersmann, Jochen

AU - Jirsa, Viktor

AU - Ritter, Petra

PY - 2022/5/1

Y1 - 2022/5/1

N2 - The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science. It offers services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional connectomes; multiscale co-simulation of spiking and large-scale networks; a domain specific language for automatic high-performance code generation from user-specified models; simulation-ready BNMs of patients and healthy volunteers; Bayesian inference of epilepsy spread; data and code 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.

AB - The Virtual Brain (TVB) is now available as open-source cloud ecosystem on EBRAINS, a shared digital research platform for brain science. It offers services for constructing, simulating and analysing brain network models (BNMs) including the TVB network simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional connectomes; multiscale co-simulation of spiking and large-scale networks; a domain specific language for automatic high-performance code generation from user-specified models; simulation-ready BNMs of patients and healthy volunteers; Bayesian inference of epilepsy spread; data and code 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.

KW - cs.CE

KW - cs.CR

KW - cs.DC

KW - q-bio.NC

KW - q-bio.QM

KW - Neuroimaging

KW - Data protection

KW - Brain modelling

KW - Connectome

KW - REPRODUCIBILITY

KW - ATLAS

KW - SPACE

KW - CONNECTOME

KW - High performance computing

KW - Network model

KW - Reproducibility

KW - Cloud

UR - https://www.scopus.com/pages/publications/85124536276

U2 - 10.1016/j.neuroimage.2022.118973

DO - 10.1016/j.neuroimage.2022.118973

M3 - Article

SN - 1053-8119

VL - 251

JO - NeuroImage

JF - NeuroImage

M1 - 118973

ER -

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

Abstract

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