Example Antimony Models

• ex_antimony_input.txt is an example input file that defines several modules each defining a genetic network, a single model that attaches them together, and an implementation of that model that tests it with real input. If you convert the file to SBML, you get several SBML files, one for each module: (Note: depending on your browser, the following .xml files may not display correctly. If not, either right-click and download them to a file, or select 'View Source'.)
  • A bistable switch
  • A feed-forward network
  • A ring oscillator
  • The combined model, and finally
  • The main module that implements the combined model.
• Conversely, an SBML oscillator was converted to Antimony using the sbml2antimony converter, producing this model.
• Finally, we have the current Curated BioModels translated to Antimony. The original models can be found at BioModels.net When the first 249 Antimony models were converted back to SBML, only one of them (model 183) produced significantly different simulation results when simulated for 10 seconds using the roadRunner simulator. Model 183 had small numerical differences for a single parameter at about 1.5 seconds (that self-corrected thereafter).
• In addition, there are several sets of Example CellML Models translated to Antimony and SBML. The original models can be found at CellML.org. These models have not been tested for numerical accuracy