BioSimulators: a central registry of simulation engines and services for recommending specific tools
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.
Keywords
Cite
@article{arxiv.2203.06732,
title = {BioSimulators: a central registry of simulation engines and services for recommending specific tools},
author = {Bilal Shaikh and Lucian P. Smith and Dan Vasilescu and Gnaneswara Marupilla and Michael Wilson and Eran Agmon and Henry Agnew and Steven S. Andrews and Azraf Anwar and Moritz E. Beber and Frank T. Bergmann and David Brooks and Lutz Brusch and Laurence Calzone and Kiri Choi and Joshua Cooper and John Detloff and Brian Drawert and Michel Dumontier and G. Bard Ermentrout and James R. Faeder and Andrew P. Freiburger and Fabian Fröhlich and Akira Funahashi and Alan Garny and John H. Gennari and Padraig Gleeson and Anne Goelzer and Zachary Haiman and Joseph L. Hellerstein and Stefan Hoops and Jon C. Ison and Diego Jahn and Henry V. Jakubowski and Ryann Jordan and Matúš Kalaš and Matthias König and Wolfram Liebermeister and Synchon Mandal and Robert McDougal and J. Kyle Medley and Pedro Mendes and Robert Müller and Chris J. Myers and Aurelien Naldi and Tung V. N. Nguyen and David P. Nickerson and Brett G. Olivier and Drashti Patoliya and Loïc Paulevé and Linda R. Petzold and Ankita Priya and Anand K. Rampadarath and Johann M. Rohwer and Ali S. Saglam and Dilawar Singh and Ankur Sinha and Jacky Snoep and Hugh Sorby and Ryan Spangler and Jörn Starruß and Payton J. Thomas and David van Niekerk and Daniel Weindl and Fengkai Zhang and Anna Zhukova and Arthur P. Goldberg and Michael L. Blinov and Herbert M. Sauro and Ion I. Moraru and Jonathan R. Karr},
journal= {arXiv preprint arXiv:2203.06732},
year = {2022}
}
Comments
6 pages, 2 figures