BioSimulations is a free platform for sharing and re-using biomodels, simulations, simulation results, and visualizations of simulation results. BioSimulations supports a wide range of frameworks (e.g., logical, Flux-Balance Analysis (FBA), continuous kinetic, discrete kinetic), simulation algorithms (e.g., FBA, SSA), model formats (e.g., SBML), and tools (e.g., COBRApy, COPASI, tellurium).
BioSimulations, developed by Jonathan Karr, Bilal Shaikh, and their team, is an online tool that makes it easy to share and reuse simulations and simulation tools for biological modeling. BioSimulations serves as a gateway for reproducible published work: it provides a central location to publish model simulations and to discover new simulation projects and tools, including resources for data visualization, and simulators that accommodate a variety of model formats and simulation algorithms. Users can use the search function to find papers and run published simulations on the site.
The web-based tools enable users to run simulations and visualize and explore results in an interactive format. It even provides tools to modify simulation experiments to generate new simulations. The platform provides support for the COMBINE/OMEX archive format, KiSAO terms, and SED-ML; building off these standardized formats makes the simulation experiments stored on BioSimulations fully transparent.
The runBioSimulations platform provides a containerized interface to ensure that authors can preview their simulations in an independent computing environment before publishing them, encouraging reproducible practices.
Biosimulations is a community-driven effort, as numerous individuals and organizations have contributed to its development. Currently, over fifty simulators are supported in the BioSimulations tool registry, with ongoing curation efforts.