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Oxford University Press, Nucleic Acids Research, W1(50), p. W108-W114, 2022

DOI: 10.1093/nar/gkac331

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

Journal article published in 2022 by Bilal Shaikh ORCID, Lucian P. Smith ORCID, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson ORCID, Eran Agmon ORCID, Henry Agnew ORCID, Steven S. Andrews ORCID, Azraf Anwar, Moritz E. Beber ORCID, Frank T. Bergmann ORCID, David Brooks ORCID, Lutz Brusch ORCID, Laurence Calzone ORCID, Kiri Choi ORCID and other authors.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

AbstractComputational 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.