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

B. Shaikh, L.P. Smith, D. Vasilescu, G. Marupilla, M. Wilson, E. Agmon, H. Agnew, S.S. Andrews, A. Anwar, M.E. Beber, F.T. Bergmann, D. Brooks, L. Brusch, L. Calzone, K. Choi, J. Cooper, J. Detloff, B. Drawert, M. Dumontier, G.B. ErmentroutJ.R. Faeder, A.P. Freiburger, F. Frohlich, A. Funahashi, A. Garny, J.H. Gennari, P. Gleeson, A. Goelzer, Z. Haiman, J. Hasenauer, J.L. Hellerstein, H. Hermjakob, S. Hoops, J.C. Ison, D. Jahn, H.V. Jakubowski, R. Jordan, M. Kalas, M. Konig, W. Liebermeister, R.S.M. Sheriff, S. Mandal, R. McDougal, J.K. Medley, P. Mendes, R. Muller, C.J. Myers, A. Naldi, T.V.N. Nguyen, D.P. Nickerson

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

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.[GRAPHICS].
Original languageEnglish
Pages (from-to)W108-W114
Number of pages7
JournalNucleic Acids Research
Volume50
Issue numberW1
Early online date7 May 2022
DOIs
Publication statusPublished - 5 Jul 2022

Keywords

  • FORMAT

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