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

Autor:	Shaikh B; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Smith LP; University of Washington, Seattle, WA 98105, USA., Vasilescu D; University of Connecticut School of Medicine, Farmington, CT 06030, USA., Marupilla G; University of Connecticut School of Medicine, Farmington, CT 06030, USA., Wilson M; University of Connecticut School of Medicine, Farmington, CT 06030, USA., Agmon E; Stanford University, Stanford, CA 94305, USA., Agnew H; LibreTexts, USA., Andrews SS; University of Washington, Seattle, WA 98105, USA., Anwar A; New York University, Brooklyn, NY 11201, USA., Beber ME; Unseen Bio ApS, 2100 København Ø, Denmark., Bergmann FT; Heidelberg University, 69120 Heidelberg, Germany., Brooks D; University of Auckland, 1010 Auckland, New Zealand., Brusch L; Technical University of Dresden, 01187 Dresden, Germany., Calzone L; Institut Curie, 75248 Paris, France., Choi K; Korea Institute for Advanced Study, 02455 Seoul, South Korea., Cooper J; University of North Carolina, Asheville, Ashville, NC 28804, USA., Detloff J; Independent, Madison, WI 53705, USA., Drawert B; University of North Carolina, Asheville, Ashville, NC 28804, USA., Dumontier M; Maastricht University, 6200 Maastricht, Netherlands., Ermentrout GB; University of Pittsburgh, Pittsburgh, PA 15260, USA., Faeder JR; University of Pittsburgh, Pittsburgh, PA 15260, USA., Freiburger AP; University of Victoria, Victoria, BC V8P 5C2, Canada., Fröhlich F; Harvard Medical School, Boston, MA 02115, USA., Funahashi A; Keio University, Yokohama 223-8522, Japan., Garny A; University of Auckland, 1010 Auckland, New Zealand., Gennari JH; University of Washington, Seattle WA 98019, USA., Gleeson P; University College London, London WC1E 6BT, UK., Goelzer A; Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France., Haiman Z; University of California, San Diego, La Jolla, CA 92093, USA., Hasenauer J; Universität Bonn, 53115 Bonn, Germany., Hellerstein JL; University of Washington, Seattle, WA 98105, USA., Hermjakob H; European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK., Hoops S; University of Virginia, Charlottesville, VA 22904, USA., Ison JC; CNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, 91000 Évry-Courcouronnes, France., Jahn D; Technical University of Dresden, 01187 Dresden, Germany., Jakubowski HV; College of Saint Benedict and Saint John's University, St. Joseph, MN 56374, USA., Jordan R; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Kalaš M; University of Bergen, 5020 Bergen, Norway., König M; Humboldt University of Berlin, 10115 Berlin, Germany., Liebermeister W; Université Paris-Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France., Sheriff RSM; European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK., Mandal S; Technical University of Dresden, 01069 Dresden, Germany., McDougal R; Yale University, New Haven, CT 06511, USA., Medley JK; Autodesk, Inc., San Rafael, CA 94903, USA., Mendes P; University of Connecticut School of Medicine, Farmington, CT 06030, USA., Müller R; Technical University of Dresden, 01187 Dresden, Germany., Myers CJ; University of Colorado at Boulder, Boulder CO, 80309, USA., Naldi A; Inria Saclay - Île-de-France Research Centre, 91120 Palaiseau, France., Nguyen TVN; European Molecular Biology Laboratory - European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK., Nickerson DP; University of Auckland, 1010 Auckland, New Zealand., Olivier BG; Vrije Universiteit Amsterdam, 1081 HZ Amsterdam, Netherlands., Patoliya D; Sarvajanik College of Engineering & Technology, Surat, Gujarat 395001, India., Paulevé L; Centre National de la Recherche Scientifique, 33400 Talence, France., Petzold LR; University of California, Santa Barbara, Santa Barbara, CA 93106, USA., Priya A; Birla Institute of Technology, Mesra, Jharkhand 835215, India., Rampadarath AK; University of Auckland, 1010 Auckland, New Zealand., Rohwer JM; Stellenbosch University, Stellenbosch, 7600, South Africa., Saglam AS; University of Pittsburgh, Pittsburgh, PA 15260, USA., Singh D; Subconscious Compute Pvt. Ltd., Bangalore, India., Sinha A; University College London, London, WC1E 6BT, UK., Snoep J; Stellenbosch University, Stellenbosch, 7600, South Africa., Sorby H; University of Auckland, 1010 Auckland, New Zealand., Spangler R; Allen Institute for Cell Science, Seattle, WA 98109, USA., Starruß J; Technical University of Dresden, 01187 Dresden, Germany., Thomas PJ; University of Utah, Salt Lake City, UT 84112, USA., van Niekerk D; Stellenbosch University, Stellenbosch, 7600, South Africa., Weindl D; Helmholtz Zentrum München GmbH and German Research Center for Environmental Health, 85764 Neuherberg, Germany., Zhang F; National Institutes of Health, Bethesda, MD 20892, USA., Zhukova A; Institut Pasteur, 75015 Paris, France., Goldberg AP; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA., Schaff JC; University of Connecticut School of Medicine, Farmington, CT 06030, USA.; Applied BioMath LLC, Concord, MA 01742, USA., Blinov ML; University of Connecticut School of Medicine, Farmington, CT 06030, USA., Sauro HM; University of Washington, Seattle, WA 98105, USA., Moraru II; University of Connecticut School of Medicine, Farmington, CT 06030, USA., Karr JR; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2022 Jul 05; Vol. 50 (W1), pp. W108-W114.
DOI:	10.1093/nar/gkac331
Abstrakt:	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. (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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