More comprehensive and more predictive models have the potential to advance biology, bioengineering, and medicine. Building more predictive models will likely require the collaborative efforts of many investigators. This requires teams to be able to share and reuse model components and simulations. Despite extensive efforts to develop standards such as COMBINE/OMEX , SBML , and SED-ML , it remains difficult to reuse many models and simulations. One challenge to reusing models and simulations is the diverse array of disparate modeling formats and simulation tools.

BioSimulators helps address this challenge by providing researchers a central place for choosing a simulation tool for a specific model and a centralized collection of containerized biosimulation tools that provide consistent command-line interfaces. Together, this collection of simulation tools provides researchers access to a wide range of simulation algorithms for a broad range of modeling frameworks and formats.

The BioSimulators standards, web application, and database support all modeling frameworks, simulation algorithms, and model formats. Currrently, BioSimulators includes tools for logical, Flux Balance Analysis (FBA), continuous kinetic (ordinary differential equations (ODE) and differential-algebraic equations (DAE)), and discrete kinetic (e.g., Stochastic Simulation Algorithms (SSA)) simulation of models that are described in using the BioNetGen Language (BNGL) , CellML , NeuroML/LEMS , pharmML , the Smoldyn Language , and the Systems Biology Markup Language (SBML) . Together, these tools support numerous simulation algorithms.

BioSimulators is implemented using several open-source tools and cloud platforms.

The containerized simulation software tools are available from the GitHub Container Registry .

The BioSimulators source code is composed of multiple open-source packages:

• BioSimulations : Code for this website, the database of simulation tools, and the REST API for querying this database.
• BioSimulators utils : Utilities for building containerized simulation tools. This provides tools for building command-line interfaces and parsing COMBINE/OMEX and SED-ML files.
• BioSimulators test suite : Tools for verifying the capabilities of containerized simulation tools.

The simulators are provided under the open-source licenses documented for each tool. The BioSimulators source code is provided under the MIT license . The licenses for BioSimulators' third-party dependencies are summarized here .

BioSimulators was developed by the Center for Reproducible Biomedical Modeling including Bilal Shaikh and Jonathan Karr at the Icahn School of Medicine at Mount Sinai ; Akhil Marupilla, Mike Wilson , Michael Blinov , and Ion Moraru at the Center for Cell Analysis and Modeling at UConn Health; and Herbert Sauro at the University of Washington.

We welcome contributions to BioSimulators!

• Simulators can be contributed by submitting GitHub issues . Please see the tutorial for information about the required format, a guide to building simulator images, and examples.
• BioSimulators software: We welcome contributions by GitHub pull requests . Please see the Guide to Contributing for information about how to get started. Please also contact the developers to coordinate potential contributions.

BioSimulators was developed with support from the Center for Reproducible Biomodeling Modeling from the National Institute of Bioimaging and Bioengineering and the National Institute of General Medical Sciences of the National Institutes of Health and the National Science Foundation .