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

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arxiv 2203.06732 v1 pith:4S6ASG4V submitted 2022-03-13 q-bio.QM cs.CEq-bio.MN

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

Bilal Shaikh , Lucian P. Smith , Dan Vasilescu , Gnaneswara Marupilla , Michael Wilson , Eran Agmon , Henry Agnew , Steven S. Andrews
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Azraf Anwar Moritz E. Beber Frank T. Bergmann David Brooks Lutz Brusch Laurence Calzone Kiri Choi Joshua Cooper John Detloff Brian Drawert Michel Dumontier G. Bard Ermentrout James R. Faeder Andrew P. Freiburger Fabian Fr\"ohlich Akira Funahashi Alan Garny John H. Gennari Padraig Gleeson Anne Goelzer Zachary Haiman Joseph L. Hellerstein Stefan Hoops Jon C. Ison Diego Jahn Henry V. Jakubowski Ryann Jordan Mat\'u\v{s} Kala\v{s} Matthias K\"onig Wolfram Liebermeister Synchon Mandal Robert McDougal J. Kyle Medley Pedro Mendes Robert M\"uller Chris J. Myers Aurelien Naldi Tung V. N. Nguyen David P. Nickerson Brett G. Olivier Drashti Patoliya Lo\"ic Paulev\'e Linda R. Petzold Ankita Priya Anand K. Rampadarath Johann M. Rohwer Ali S. Saglam Dilawar Singh Ankur Sinha Jacky Snoep Hugh Sorby Ryan Spangler J\"orn Starru{\ss} Payton J. Thomas David van Niekerk Daniel Weindl Fengkai Zhang Anna Zhukova Arthur P. Goldberg Michael L. Blinov Herbert M. Sauro Ion I. Moraru Jonathan R. Karr
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classification q-bio.QM cs.CEq-bio.MN
keywords toolsbiosimulatorssimulationhelpregistrycentralcombinefind
verification ladder T0 review T1 audit T2 compute T3 formal T4 reserved
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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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