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

Area of Science:

• Computational biology
• Bioinformatics
• Biomedical engineering

Background:

• Computational models accelerate bioscience, bioengineering, and medicine.
• Simulation tool reuse and reproducibility are hindered by diverse formats and siloed software.
• Distinct interfaces for each simulation tool complicate access and integration.

Purpose of the Study:

• To develop a centralized registry and standardized interfaces for computational simulation tools.
• To improve the discoverability, usability, and interoperability of simulation software in life sciences.
• To facilitate the exchange, reproduction, and combination of biological simulations.

Main Methods:

• Developed BioSimulators, a registry of simulation tool capabilities.
• Created consistent Python, command-line, and containerized interfaces for simulation tools.
• Utilized standards like CellML, SBML, SED-ML, and COMBINE archives.
• Implemented validation tools for simulation projects and tools.
• Developed recommendation services for tool discovery.

Main Results:

• Established BioSimulators as a central registry for simulation tools.
• Provided standardized interfaces for accessing and executing various simulation software.
• Ensured consistent use of standards through validation tools.
• Enabled recommendation services to aid tool selection for specific modeling projects.

Conclusions:

• BioSimulators enhances the exchange, reproduction, and combination of biological simulations.
• The platform addresses key challenges in computational modeling for bioscience and medicine.
• Standardization and consistent interfaces are crucial for advancing simulation-based research.