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Meet our new Reproducibility Portal: a more user-friendly way to interact with the BioSim database!

Powerful biomodel simulations and tools at your fingertips

Generate, share, and re-use biomodels, simulations, results, and visualizations like never before with our free registry of biosimulation tools.

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In Collaboration With

Karr Lab at Mount SinaiNational Institute of Biomedical Imaging and BioengineeringModelDB Computational NeuroscienceNational Science FoundationUniversity of WashingtonUConn Health Center for Cell Analysis & ModelingCenter for Reproducible Biomedical ModelingBioModels DatabaseBiGG Models KnowledgebaseIcahn School of Medicine at Mount SinaiJWS Online Cellular Systems ModelingResource Balance AnalysisNational Institutes of Health
Karr Lab at Mount SinaiNational Institute of Biomedical Imaging and BioengineeringModelDB Computational NeuroscienceNational Science FoundationUniversity of WashingtonUConn Health Center for Cell Analysis & ModelingCenter for Reproducible Biomedical ModelingBioModels DatabaseBiGG Models KnowledgebaseIcahn School of Medicine at Mount SinaiJWS Online Cellular Systems ModelingResource Balance AnalysisNational Institutes of Health
Karr Lab at Mount SinaiNational Institute of Biomedical Imaging and BioengineeringModelDB Computational NeuroscienceNational Science FoundationUniversity of WashingtonUConn Health Center for Cell Analysis & ModelingCenter for Reproducible Biomedical ModelingBioModels DatabaseBiGG Models KnowledgebaseIcahn School of Medicine at Mount SinaiJWS Online Cellular Systems ModelingResource Balance AnalysisNational Institutes of Health
Karr Lab at Mount SinaiNational Institute of Biomedical Imaging and BioengineeringModelDB Computational NeuroscienceNational Science FoundationUniversity of WashingtonUConn Health Center for Cell Analysis & ModelingCenter for Reproducible Biomedical ModelingBioModels DatabaseBiGG Models KnowledgebaseIcahn School of Medicine at Mount SinaiJWS Online Cellular Systems ModelingResource Balance AnalysisNational Institutes of Health

BioSimulations was developed by the Center for Reproducible Biomedical Modeling , the Karr Lab at the Icahn School of Medicine at Mount Sinai , and the Center for Cell Analysis & Modeling at the University of Connecticut Health Center with support from the National Institutes of Health and the National Science Foundation.

Built Using These Awesome Projects & Platforms

COMBINE StandardsCOPASI Biochemical Network SimulatorGitHubModeling Tools GroupNestJS FrameworkNetlify Cloud PlatformBioSimulators RegistryFont AwesomeBioSimulations EcosystemKubernetes Container OrchestrationDocker Container EngineOpenAPI Swagger SpecificationsMaterial DesignAuth0 Identity PlatformMongoDB DatabasePlotly Scientific VisualizationsAngular Web Framework
COMBINE StandardsCOPASI Biochemical Network SimulatorGitHubModeling Tools GroupNestJS FrameworkNetlify Cloud PlatformBioSimulators RegistryFont AwesomeBioSimulations EcosystemKubernetes Container OrchestrationDocker Container EngineOpenAPI Swagger SpecificationsMaterial DesignAuth0 Identity PlatformMongoDB DatabasePlotly Scientific VisualizationsAngular Web Framework
COMBINE StandardsCOPASI Biochemical Network SimulatorGitHubModeling Tools GroupNestJS FrameworkNetlify Cloud PlatformBioSimulators RegistryFont AwesomeBioSimulations EcosystemKubernetes Container OrchestrationDocker Container EngineOpenAPI Swagger SpecificationsMaterial DesignAuth0 Identity PlatformMongoDB DatabasePlotly Scientific VisualizationsAngular Web Framework
COMBINE StandardsCOPASI Biochemical Network SimulatorGitHubModeling Tools GroupNestJS FrameworkNetlify Cloud PlatformBioSimulators RegistryFont AwesomeBioSimulations EcosystemKubernetes Container OrchestrationDocker Container EngineOpenAPI Swagger SpecificationsMaterial DesignAuth0 Identity PlatformMongoDB DatabasePlotly Scientific VisualizationsAngular Web Framework

BioSimulations is implemented using several open-source tools and cloud platforms. The models, simulations, and visualizations are available under the licenses specified for each resource. The code is openly available under the MIT license. The simulation tools provided are available under the licenses specified for each simulation tool at BioSimulators.

What is BioSimulations?

A Revolutionary Platform

BioSimulations is the free platform for discovering and comparing simulators, sharing and re-using biomodels, running simulations, and browsing/sharing/visualizing simulation results. With simulators and simulations on one platform, researchers have access to streamlined workflows to accelerate their discoveries.
Simulators
Access a registry of biosimulation tools encompassing diverse frameworks, algorithms, and model formats curated to streamline the simulation process. The registry, powered by conventions like SED-ML, offers readily available Python packages, command-line programs, and Docker images for consistent execution.
Get StartedBrowse Simulators
Simulations
Access 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) and connect with a community of others supercharging their bio-data processing.
Run a SimulationBrowse Simulation Runs

Your Workflow, Your Way

Starting from scratch? BioSimulations offers a nuts-to-bolts pipeline. Ready to import and upgrade some data? BioSimulations has extensive documentation to make supercharging your bio data easy.

Run a Simulation

Discover & Compare Simulators

Browse Simulations

Submit a Simulation

Convert a File

REST API

Documentation