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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:

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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!

1 comment:

MLB2k11 said...

Lot of useful points are there. Its really keeps me updated.
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