BioSimulators is a free registry of biosimulation tools. The registry includes tools for a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and model formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). Many of the simulation tools provide Python packages, command-line programs, and Docker images with consistent interfaces. Together, BioSimulators makes it easier to run simulations. BioSimulators is powered by several conventions including SED-ML BioSimulators makes it easy to find tools that can run specific simulations and download and run them. The tools in the BioSimulators registry can run a broad range of modeling frameworks, simulation algorithms, and model formats. BioSimulators makes it easier for developers to compare simulation tools. This can be used to identify the strengths of different approaches, find bugs, and drive standardization.
Quick Start

Getting started with BioSimulators is easy! Explore our documentation for a comprehensive guide and best practices.

CLI with Python
You can easily run a BioSimulator from the command-line in as little as 3 simple steps:

1. Install the BioSimulator you want with pip. Here we will use biosimulators-tellurium. A full list of BioSimulators packages can be found here. 


                    % pip install biosimulators-tellurium

2. Run the following from the command line, passing an OMEX filepath as -i and the output dir as -o 


                    % biosimulators-tellurium \
                      -i ~/experiments/my-file.omex \
                      -o ~/Desktop/results

3. Go to the directory and view your results.


                    % cd ~/Desktop/results
CLI with Docker
You can easily run the same BioSimulator simulation with Docker: 

                    % docker pull \
                        ghcr.io/biosimulators/tellurium:2.2.8
                  

                    % docker run \
                        ghcr.io/biosimulators/tellurium:2.2.8 \
                        -i /path/to/archive.omex \
                        -o /path/to/outputs
Programmatically with Python
You can also easily run a BioSimulator programmatically with Python:

1. Import the desired BioSimulator.


                    import biosimulators_tellurium as bt

2. Define the paths to both your OMEX file and desired output destination:


                    omex = 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'
                  

                    results_dir = '/content/my_results'

3. Run the simulation and get the results and log. Print the results:


                    results, log = bt.exec_sedml_docs_in_combine_archive(
                          omex,
                          results_dir,
                          config
                    )

                    print(results)
                    print(log)

This is the full implementation:


                    import biosimulators_tellurium as bt

                    omex = 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'
                    results_dir = '/content/my_results'
                    results, log = bt.exec_sedml_docs_in_combine_archive(
                          omex,
                          results_dir,
                          config
                    )

                    print(results)
                    print(log)
In your browser with Binder
A fully interactive Binder tutorial is available here.
Consistent access to multiple modeling frameworks, algorithms, formats & tools
About BioSimulators

BioSimulators 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.

BioSimulators is implemented using several open-source tools and cloud platforms. The simulators are available under the licenses specified for each simulator. The BioSimulators code is openly available under the MIT license .

Please see the documentation for more information.