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, Azraf Anwar,, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence, Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert

TL;DR
BioSimulators is a centralized registry that standardizes and catalogs simulation tools in biosciences, facilitating easier discovery, reproducibility, and reuse of computational models across various formats and interfaces.
Contribution
It introduces a comprehensive registry with standardized interfaces and validation tools, improving tool discoverability and reproducibility in bioscience simulations.
Findings
Established a central registry of simulation tools
Developed standardized interfaces for multiple tools
Enabled recommendation services for tool selection
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…
Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.
