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 share and reuse models and simulations. One challenge to sharing and reusing models is the disparate formats, model repositories, and simulation tools for different types of models. The proliferation of numerous similar formats, repositories, and tools makes it difficult, especially for non-experts, to find models and to find an appropriate simulation tool for each model. In addition, the existing model repositories have limited capabilities for sharing associated resources such as training data, simulation experiments, and visualizations.

BioSimulations addresses these challenges by making it easier for researchers to share and reuse models. First, BioSimulations provides authors a central portal for sharing models, simulations, and visualizations. Importantly, authors can share models in any format, authors can share simulations that require any simulator, and authors can share arbitrarily complex visualizations. Second, BioSimulations provides researchers a central portal for finding models and a simple web interface for reusing any model, simulation, or visualization. This is achieved using BioSimulators, a collection of Docker images that abstract the details of multiple modeling frameworks, simulation algorithms, model formats, and simulation tools.

BioSimulations supports all modeling frameworks and model formats. However, currrently BioSimulations can only simulate 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)) models that are described in using the BioNetGen Language (BNGL) or the Systems Biology Markup Language (SBML) .

BioSimulations uses the BioSimulators collection of simulation tools to simulate models. Through BioSimulators, BioSimulations supports a numerous algorithms for simulating logical, FBA, and kinetic models. BioSimulators builds upon Docker and BioContainers . Please see BioSimulators for more information about supported modeling frameworks, simulation algorithms, model formats, and simulation software tools.

In addition to models, simulations, and visualizations contributed by investigators, BioSimulations contains models, simulations, and visualizations imported from BiGG , BioModels , and Cell Collective . BioSimulations provides a central place to find and reuse these models.

BioSimulations provides basic capabilities for reproducing and reusing a wide range of biomodeling projects. For further exploration, we encourage users to use the domain-specific online platforms, desktop programs, and libraries outlined below.

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

The models, simulations, and visualizations in BioSimulations can be programmatically obtained using our REST API . Documentation for the API is available at the same URL.

The containerized simulation software tools are available from BioSimulators .

The BioSimulations source code is composed of the following open-source packages:

• BioSimulations : Core functionality
• BioSimulations utils : Utilities for encoding simulation experiments into SED-ML, encoding simulations studies in COMBINE/OMEX archives, and testing simulator images.

The models, simulations, and visualizations in BioSimulations are provided under the license specified for each resource. The containerized simulators are provided under the open-source licenses documented for each image. Please see BioSimulators for more information. The BioSimulations source code is provided under the MIT license . The licenses for BioSimulations' third-party dependencies are summarized here .

BioSimulations 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 BioSimulations!

• Models, simulations, and visualizations can be contributed through this website or our REST API. Please create an account to get started.
• 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.
• BioSimulations 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.

BioSimulations 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 .