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

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 particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.