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 and repositories such as BioModels, it is still often difficult to reuse models and simulations. One challenge to sharing and reusing models is the disparate formats and simulation tools for different types of models. The proliferation of numerous similar formats and tools makes it difficult, especially for non-experts, to find an appropriate simulation tool for each model.

runBioSimulations addresses this challenge by providing researchers a simple web interface for executing a wide range of models that use a wide range of modeling frameworks, simulation algorithms, and modeling formats. This is achieved using BioSimulators, a collection of Docker images that provide standardized access to a variety of simulation tools that collectively support multiple modeling frameworks, simulation algorithms, and modeling formats.

runBioSimulations provides basic capabilities for executing simulations and visualizing their results. In addition to these features, the full-featured BioSimulations web application will enable authors to publish models, simulations, and visualizations. BioSimulations will also provide users a central place to find and reuse published models, simulations, and visualizations. runBioSimulations is ideal for investigators who wish to execute simulations privately during the course of their research. The full-featured application is ideal for investigators who want to publish modeling studies or reuse published studies.

runBioSimulations can execute a broad range of modeling frameworks, simulation algorithms, and modeling formats. runBioSimulations uses the BioSimulators collection of simulation tools to execute modeling projects. Through BioSimulators, runBioSimulations supports numerous algorithms for simulating logical, FBA, and kinetic models. BioSimulators builds upon Docker images . Please see BioSimulators for more information about the supported modeling frameworks, simulation algorithms, modeling formats, and simulation software tools.

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

The containerized simulation software tools are available from BioSimulators .

The source code for runBioSimulations is available from GitHub .

The source code is provided under the MIT license . The licenses for runBioSimulations' third-party dependencies are summarized here . The simulator images are provided under the open-source licenses documented for each image. Please see BioSimulators for more information.

runBioSimulations 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 runBioSimulations!

• Containerized simulators can be contributed by submitting GitHub issues . Please see BioSimulators for information about the required format, a guide to building simulator images, and examples.
• runBioSimulations 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.

runBioSimulations 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 .