BioSimulations supports all modeling frameworks. However, currently BioSimulations can only simulate the 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)) frameworks. This includes rule-based models. BioSimulations uses the BioSimulators collection of simulation tools to simulate models. Please see BioSimulators

for more information about supported modeling frameworks.

Models can be shared in any format. However, currently BioSimulations can only simulate models encoded in the BioNetGen Language (BNGL)

and the Systems Biology Markup Language (SBML)

. BioSimulations uses the BioSimulators collection of simulation tools to simulate models. Please see BioSimulators

for more information about supported model formats.

Currently, BioSimulations can only simulate models that use core and Flux Balance Constraints (fbc)

or Qualitative Models (qual)

packages.

Yes! Multiple models (potentially involving multiple model languages, multiple simulation algorithms, and/or multiple simulation tools) could be combined together. To co-simulate multiple models, we recommend using the Python APIs for the BioSimulators simulation tools because they provide consistent and flexibile interfaces to many simulation tools. Specifically, we recommend using the Vivarium framework to combine multiple models and/or simulation tools. Vivarium also provides tooling to use BioSimulators and BioSimulations.

BioSimulations supports numerous algorithms for simulating 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. BioSimulations uses the BioSimulators collection of simulation tools to simulate models. Please see BioSimulators

for more information about supported simulation algorithms.

BioSimulations provides a form for describing simulations. Internally, BioSimulations represents simulations using its own format which is similar to Simulation Experiment Description Markup Language (SED-ML)

. BioSimulations can export simulations to SED-ML.

Please submit an issue

to request support for another modeling framework.

Please submit an issue

to request support for another algorithm.

Please submit an issue

to request support for another model format.

BioSimulations stores results permanently.

To ensure the provenance of simulation results, simulation results can only be generated by BioSimulations.

To credit authors for their contributions, this web application requires an account to execute simulations. Please use our standalone web application at {{ config.dispatchAppUrl }} or standalone web service at {{ config.dispatchApiUrl }} to execute COMBINE archives without an account. This web application and this web service provide the same simulation capabilities (programs and algorithms) as this web application through simpler interfaces. These simpler interface don't require accounts, and they only have the capability to execute simulations and visualize their results.

BioSimulations uses the BioSimulators collection of containerized simulation software tools. Please see https://biosimulators.org for information about the available simulation tools, including the modeling frameworks, simulation algorithms, and model formats supported by each tool.

BioSimulations uses the BioSimulators collection of containerized simulation software tools. These containers make it easy to execute simulations by all providing the same command-line interface. The containers are easy to install and run on your own machine. The containers can be used on top of any operating system. Please see https://biosimulators.org for more information about how to install and run these containers.

Currently, simulations can only be uploaded in Vega format

Currently, BioSimulations supports the Creative Commons licenses

Please submit an issue

to request support for another license.

Please contact us via email

to request edits to published a model, simulation, or visualization.

To ensure the community has permanent access to published resources, published models, simulations, and visualizations cannot be deleted.