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Shaikh, B.* ; Smith, L.P.* ; Vasilescu, D.* ; Marupilla, G.* ; Wilson, M.* ; Agmon, E.* ; Agnew, H.* ; Andrews, S.S.* ; Anwar, A.* ; Beber, M.E.* ; Bergmann, F.T.* ; Brooks, D.* ; Brusch, L.* ; Calzone, L.* ; Choi, K.* ; Cooper, J.* ; Detloff, J.* ; Drawert, B.* ; Dumontier, M.* ; Ermentrout, G.B.* ; Faeder, J.R.* ; Freiburger, A.P.* ; Fröhlich, F.* ; Funahashi, A.* ; Garny, A.* ; Gennari, J.H.* ; Gleeson, P.* ; Goelzer, A.* ; Haiman, Z.* ; Hasenauer, J.* ; Hellerstein, J.L.* ; Hermjakob, H.* ; Hoops, S.* ; Ison, J.C.* ; Jahn, D.* ; Jakubowski, H.V.* ; Jordan, R.* ; Kalaš, M.* ; König, M.* ; Liebermeister, W.* ; Sheriff, R.S.M.* ; Mandal, S.* ; McDougal, R.* ; Medley, J.K.* ; Mendes, P.* ; Müller, R.* ; Myers, C.J.* ; Naldi, A.* ; Nguyen, T.V.N.* ; Nickerson, D.P.* ; Olivier, B.G.* ; Patoliya, D.* ; Paulevé, L.* ; Petzold, L.R.* ; Priya, A.* ; Rampadarath, A.K.* ; Rohwer, J.M.* ; Saglam, A.S.* ; Singh, D.* ; Sinha, A.* ; Snoep, J.D.* ; Sorby, H.* ; Spangler, R.* ; Starruß, J.* ; Thomas, P.J.* ; van Niekerk, D.* ; Weindl, D. ; Zhang, F.* ; Zhukova, A.* ; Goldberg, A.P.* ; Schaff, J.C.* ; Blinov, M.L.* ; Sauro, H.M.* ; Moraru, I.I.* ; Karr, J.R.*

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

Nucleic Acids Res. 50, W108-W114 (2022)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
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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Publication type Article: Journal article
Document type Scientific Article
Language english
Publication Year 2022
HGF-reported in Year 2022
ISSN (print) / ISBN 0305-1048
e-ISSN 1362-4962
Journal Nucleic Acids Research
Quellenangaben Volume: 50, Issue: W1, Pages: W108-W114 Article Number: , Supplement: ,
Publisher Oxford University Press
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
POF-Topic(s) 30205 - Bioengineering and Digital Health
Research field(s) Enabling and Novel Technologies
PSP Element(s) G-553800-001
Grants NIBIB
NIH HHS
DOI 10.1093/nar/gkac331
WOS ID WOS:000791760200001
Scopus ID 85134730260
PubMed ID 35524558
Erfassungsdatum 2022-06-10
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