Documentation about modeling frameworks, simulation algorithms, model formats, and simulation tools
REST API documentation

Below is a collection of brief tutorials on runBioSimulations:

  • Creating COMBINE archives with SED-ML documents for simulation experiments.
  • Finding simulations tools that have the capabilities to execute specific COMBINE archives.
  • Using this application or its API to execute COMBINE archives.
  • Checking the status of simulations.
  • Retrieving the results of simulations.
  • Visualizing the results of simulations.
Live tutorials

The BioSimulations Team also periodically presents live tutorials. See below for a schedule of upcoming events and recordings of past events, or contact the BioSimulations Team to arrange a tutorial.

Click here to load several example simulation projects (COMBINE/OMEX files) from the BioSimulators test suite . These simulation projects are verified to be compatible with runBioSimulations. The BioSimulators test suite describes the specific simulation tools that are compatible with each example project.

runBioSimulations requires modeling projects (one or more simulations typically in SED-ML format of one or more models) to be described by an OMEX file and packaged into a COMBINE archive. Several examples COMBINE/OMEX archives are available here .

COMBINE/OMEX files which describe modeling projects can be obtained from model repositories such as BioModels . However, most of the COMBINE/OMEX files currently available from BioModels are invalid. We are working with the BioModels Team to correct these files.

COMBINE/OMEX archives can be created with several simulation tools such as those listed below. Note, due to divergence between these tools and the specifications of the COMBINE/OMEX archive and SED-ML formats (see FAQs), runBioSimulations cannot execute all COMBINE/OMEX archives that can be created with these tools. We are working the community to address these issues.

  • COPASI
  • iBioSim
  • JWS Online
  • tellurium
  • VCell

Alternatively, new COMBINE/OMEX archives can be created by following these steps:

  1. Create a directory for the modeling project.
  2. Create one or more models: Create files which describe the models that you would like to simulate and save these files to the directory for the modeling project. For example, the BioNetGen Language (BNGL) and Systems Biology Markup Language (SBML) formats can be used to represent models of biochemical networks. More information about BNGL and SBML is available from their websites. Alternatively, models can be obtained from BioModels and other model repositories.
  3. Create or more simulations: Create a Simulation Experiment Description Markup Language (SED-ML) file which describes the simulations that you would like to execute and the simulation results that you would like to record. Currently, all of the simulation tools support a subset of SED-ML including one step and timecourse simulations (sedml:OneStep and sedml:UniformTimeCourse), individual simulation tasks (sedml:Task), data generators for time and individual variables (sedml:DataGenerator), and report outputs (sedml:Report). Some of the simulation tools support the full SED-ML specification including steady-state simulations (sedml:SteadyState), repeated tasks (sedml:RepeatedTask), data generators for mathematical expressions (sedml:DataGenerator), and plot outputs (sedml:Plot2d and sedml:Plot3d). Save these files to the directory for the modeling project. More information about SED-ML is available from the SED-ML website. Alternatively, simulations can be obtained from the BioSimulations repository of modeling projects .
  4. Create an OMEX file which describes your model and simulation files and package them into a COMBINE archive file: OMEX is a format for describing a collection of modeling files, and a COMBINE archive is a zip file which contains an OMEX file and all of the other files which comprise the modeling project. Several example COMBINE archives are available here . More information about the OMEX and COMBINE formats is available at the COMBINE website . The COMBINE website lists several software tools for creating COMBINE archives including COMBINE Archive and COMBINE Archive Web .
runBioSimulations uses the BioSimulators collection of simulation tools. These tools each support different modeling frameworks, different simulation algorithms, and different model formats. The BioSimulators website outlines the modeling frameworks, simulation algorithms, and model formats supported by each tool. After determining the framework and format of your model and the simulation algorithm which you would like to execute, use this website to identify a simulation tool which is capable of executing your modeling project.

Please follow these steps to execute a modeling project:

  1. Open the project submission form.
  2. Select a COMBINE/OMEX file to execute.
  3. Select a simulation tool and a specific version of that tool.
  4. Enter a name for your project. We recommend choosing a descriptive name that will help you recall the purpose of your project. These names will be particularly helpful if you run multiple projects.
  5. Optionally, enter your email address to receive notification when your project has completed and is ready for your analysis.
  6. Click the "Run" button. After you click the "Run" button, you will receive a URL where you will be able to view the status of your project and retrieve and visualize its results. If you provided an email address, you will be notified by email when your project has completed. This email will contain the same URL.

Please follow these steps to view the status of a project:

  1. Open the URL provided after you submitted your project.
  2. Click the "Overview" tab to view the status of the project.
  3. Once the project has completed, click the "Log" tab to view the console log for the execution of the project.

After your project has completed, please follow these steps to retrieve its results:

  1. Open the URL provided after you submitted your project.
  2. Click the results icon to download the results of the project as a zip archive. This archive will contain a file for each report specified in each SED-ML file in the COMBINE/OMEX archive for your project.

After your project has completed, please follow these steps to visualize its results:

  1. Open the URL provided after you submitted your project.
  2. Click the "Design chart" tab to open a form for choosing which results to visualize.
  3. Select one of the SED-ML files in your project.
  4. Select one of the reports in the selected SED-ML file. This will display a time series chart of the selected report.
  5. Use the controls in the chart to customize the chart. For example, the controls can be used to view specific variables or zoom into the chart.
In addition to this web application, a REST API for executing projects is available at {{ config.dispatchApiUrl }}. This API supports the same simulation tools as this web application.

We welcome contributions to the runBioSimulations platform (e.g., web application, REST API, database, simulation services)! Please see the Guide to Contributing for information about how to contribute to the runBioSimulations.

The BioSimulations Team periodically presents live tutorials. Below is the schedule of upcoming events and recordings of past events.

  • 2021-10-11 - 2021-10-15: COMBINE Conference
  • 2021-07-23: Network Modeling Virtual Summer School & Symposium
    • Video
  • 2021-03-22: HARMONY Hackathon
    • Video
    • Slides