SED-ML in Pictures

Today a question came up on the sbml-discuss list on freely available software for simulating BioModels 139 and BioModel 140. Someone tried to reproduce the simulation results with these models and failed to do so. In the future of course SED-ML will help us out in these cases, by essentially encoding the simulation experiment directly.

So I went ahead and created some SED-ML examples for these models. You will find them below. Admittedly, so far only our tools seem to support the format, but other groups are showing interest. To give it a try, you could download the latest version of the Systems Biology Workbench. Once it is installed, start the ‘Simulation Tool’. Which now comes with an experimental support for SED-ML, and there you can open and run SED-ML files from the ‘SED-ML’ tab.

Here is how it looks for the BioModel 139:

And here the result for BioModel 140:

Of course SED-ML is still in its infancy, but as you can see, there is a need for it now. So don’t wait for the final version, start implementing it in your tools now! Or if you don’t develop for a software package yourself, ask the authors of your favorite tool to do so!

BioModel 139:

• SED-ML Script Version
• SED-ML (XML)
• SED-ML (XML archive) 

BioModel 140:

• SED-ML Script Version
• SED-ML (XML)
• SED-ML (XML archive)