Select a method for providing a COMBINE/OMEX archive which describes one or more simulations (in SED-ML format) of one or more models (e.g., in BNGL, SBML formats). COMBINE/OMEX files can either be uploaded from your local computer or loaded from a publicly-accessible URL.

Uploaded archives are limited to 64 MB. Archives up to 1 GB can be submitted via URLs.

A form for creating COMBINE/OMEX archives and SED-ML files from model files is available here. COMBINE/OMEX archives can also be created with simulation tools such as COPASI and VCell . Additional information about obtaining and creating COMBINE/OMEX archives is available in the help and FAQ. The help includes recommendations for additional software tools for authoring COMBINE/OMEX archives and SED-ML files. The FAQ includes information about known incompatibilities among COMBINE/OMEX archives and SED-ML files created with different tools.

Click here to load several example simulation projects from the BioSimulators test suite .

Select a simulation tool which is capable of executing your archive and a version of that tool. This tool must support all of the model formats (e.g., BNGL, SED-ML) and simulation algorithms (e.g., ODE, SSA) involved in your archive.

Because each tool supports a different set of formats and algorithms, your archive is likely only compatible with a subset of the available simulation tools.

The README for the BioSimulators test suite outlines the simulator compatibility of several of the example archives in the test suite.

BioSimulators describes the modeling formats (e.g., COMBINE/OMEX, SBML, SED-ML), modeling frameworks (e.g., logical, FBA, kinetic), and simulation algorithms (e.g., ODE, SSA) that each simulation tool supports. We recommend using BioSimulators to determine which tools are capable of executing your archive.

Some simulation tools, such as COBRApy and RBApy, can optionally execute simulations using commercial solvers such as Gurobi . These commercial solvers are often more accurate and more performant. However, these commercial solvers are not required to execute any of the available simulation tools. All of the available simulation tools can be run with freely available solvers.

Optionally, users can use these commercial solvers for academic research and education. To use these commercial solvers, check the box above to confirm that you are using runBioSimulations for academic research or education.

Non-academic users can execute simulations with commercial solvers by (a) running simulations through runBioSimulations' API and providing license keys through environment variables or (b) using the Docker images, command-line programs, or Python APIs for simulation tools on their own machines with their own license key environment variables or license files.