Download Links

Simulate 3D | SBW (Win32) | Bifurcation Discovery | FluxBalance

Sunday, June 26, 2011

SED-ML Web Tools, SED-ML Script Editor & CellML Simulation Support

I’ve just upgraded the SED-ML Web Tools to a newer version.

This version includes several bug fixes, as well as an experimental version of CellML simulation support. The CellML simulation support is thanks to an executable based on the CellML API provided by David Nickerson.

To accommodate this there have been several changes to the LibSedML API, where previously the API would have properties like .SBML or functions like GetSBMLId(), now these functions are hidden behind a native interface IModelingLanguage that will be populated based on the Model source URN as provided in the SED-ML file. This should make it easy to provide support for other languages such as NeuroML and VCellML as well.

I have also released a new version of the SED-ML Script editor. It now allows to open SBML or CellML files directly, for which then a rudimentary SED-ML file will be generated. Later it can be modified for more complex experiments. It also provides SED-ML validation capabilities. This time it is a windows only release (since I only have the CellML simulator as windows binary). It is available from SourceForge:


Sunday, June 12, 2011

Introducing the SED-ML Web Tools

I’ve spend the weekend working on a new set of tools for simulating and Validating SED-ML files. They are online now under:

Let us first take a brief tour around the site:

Unable to display content. Adobe Flash is required.

Let me point just a couple of things.


The current implementation will only simulate SBML files, using RoadRunner. As soon as I find time to update it I will add additional simulators. Currently 3D plots won’t work either. And of course simulation will only work if the model files are either:

  • accessible via URNs
  • accessible via WEB
  • included in the archive.

Simulation already implements the Nested Simulation Proposal.


The new thing about the validation is that it also provides an option to fix common errors. This feature can be used to upgrade SED-ML files that were created before SED-ML L1V1 was released! Simply click on ‘Fix common errors’, and then download the file again.


Stay tuned for further updates, the next steps will be to Create and Edit simulation experiment descriptions. Also planned are web services that make it easy to create SED-ML files!