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Article Dans Une Revue Nucleic Acids Research Année : 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Bilal Shaikh (1) , Lucian Smith (2) , Dan Vasilescu (3) , Gnaneswara Marupilla (3) , Michael Wilson (3) , Eran Agmon (4) , Henry Agnew (5) , Steven Andrews (2) , Azraf Anwar (6) , Moritz Beber (7) , Frank Bergmann (8) , David Brooks (9) , Lutz Brusch (10) , Laurence Calzone (11) , Kiri Choi (12) , Joshua Cooper (13) , John Detloff , Brian Drawert (13) , Michel Dumontier (14) , G Bard Ermentrout (15) , James Faeder (15) , Andrew Freiburger (16) , Fabian Fröhlich (17) , Akira Funahashi (18) , Alan Garny (9) , John Gennari (2) , Padraig Gleeson (19) , Anne Goelzer (20) , Zachary Haiman (21) , Jan Hasenauer (22) , Joseph Hellerstein (2) , Henning Hermjakob (23) , Stefan Hoops (24) , Jon Ison (25) , Diego Jahn (10) , Henry Jakubowski (26) , Ryann Jordan (1) , Matúš Kalaš (27) , Matthias König (28) , Rahuman Sheriff (23) , Synchon Mandal (10) , Robert Mcdougal (29) , J Kyle Medley (30) , Pedro Mendes (3) , Robert Müller (10) , Chris Myers (31) , Aurélien Naldi (32) , Tung Nguyen (23) , David Nickerson (9) , Brett Olivier (33) , Drashti Patoliya (34) , Loïc Paulevé (35) , Linda Petzold (36) , Ankita Priya (37) , Anand Rampadarath (9) , Johann Rohwer (38) , Ali Saglam (15) , Dilawar Singh (39) , Ankur Sinha (19) , Jacky Snoep (38) , Hugh Sorby (9) , Ryan Spangler (40) , Jörn Starruss (10) , Payton Thomas (41) , David van Niekerk (38) , Daniel Weindl (42) , Fengkai Zhang (43) , Anna Zhukova (44) , Arthur Goldberg (1) , James Schaff (3, 45) , Michael Blinov (3) , Herbert Sauro (46) , Ion Moraru (3) , Jonathan r Karr (1)
1 MSSM - Icahn School of Medicine at Mount Sinai [New York]
2 University of Washington [Seattle]
3 UCONN - University of Connecticut
4 Stanford University
5 LibreTexts
6 NYU - New York University [New York]
7 Unseen Bio ApS
8 Universität Heidelberg [Heidelberg] = Heidelberg University
9 University of Auckland [Auckland]
10 TU Dresden - Technische Universität Dresden = Dresden University of Technology
11 Centre de recherche de l'Institut Curie [Paris]
12 KIAS - Korea Institute for Advanced Study
13 UNC - University of North Carolina System
14 Maastricht University [Maastricht]
15 PITT - University of Pittsburgh
16 UVIC - University of Victoria [Canada]
17 HMS - Harvard Medical School [Boston]
18 Keio University [Tokyo]
19 UCL - University College of London [London]
20 MaIAGE - Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas]
21 UC San Diego - University of California [San Diego]
22 UKB - Universitätsklinikum Bonn
23 EMBL-EBI - European Bioinformatics Institute [Hinxton]
24 University of Virginia
25 IFB-CORE - Institut Français de Bioinformatique
26 College of Saint Benedict and Saint John's University
27 UiB - University of Bergen
28 HU Berlin - Humboldt-Universität zu Berlin = Humboldt University of Berlin = Université Humboldt de Berlin
29 Yale University [New Haven]
30 Autodesk
31 University of Colorado [Boulder]
32 Lifeware - Computational systems biology and optimization
33 VU - Vrije Universiteit Amsterdam [Amsterdam]
34 Sarvajanik College of Engineering & Technology
35 CNRS - Centre National de la Recherche Scientifique
36 UC - University of California
37 BIT Mesra - Birla Institute of Technology [Mesra]
38 Stellenbosch University
39 Subconscious Compute Pvt
40 Allen Institute for cell sciences
41 University of Utah
42 Helmholtz Zentrum München = German Research Center for Environmental Health
43 NIH - National Institutes of Health [Bethesda, MD, USA]
44 IP - Institut Pasteur [Paris]
45 Applied Biomathematics [New York]
46 University of Mary Washington
Lucian Smith
Michael Wilson
Eran Agmon
Henry Agnew
Steven Andrews
Moritz Beber
David Brooks
Kiri Choi
John Detloff
  • Fonction : Auteur
Brian Drawert
Michel Dumontier
G Bard Ermentrout
James Faeder
Andrew Freiburger
Fabian Fröhlich
Akira Funahashi
Alan Garny
John Gennari
Padraig Gleeson
Zachary Haiman
Jan Hasenauer
Joseph Hellerstein
Stefan Hoops
Jon Ison
Matúš Kalaš
Robert Mcdougal
J Kyle Medley
  • Fonction : Auteur
Pedro Mendes
Chris Myers
David Nickerson
Brett Olivier
Linda Petzold
Anand Rampadarath
Johann Rohwer
Ali Saglam
Dilawar Singh
Ankur Sinha
Jacky Snoep
Hugh Sorby
Ryan Spangler
Payton Thomas
David van Niekerk
Anna Zhukova
Michael Blinov
Herbert Sauro
Ion Moraru

Résumé

Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.
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hal-03666382 , version 1 (12-05-2022)

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Bilal Shaikh, Lucian Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, et al.. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research, 2022, pp.1-7. ⟨10.1093/nar/gkac331⟩. ⟨hal-03666382⟩
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