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Wednesday, March 3, 2010

Supporting SED-ML

SED-ML, the Simulation Experiment Description – Markup Language, offers the possibility to exchange simulation experiments. That is, instead of receiving a model and wondering how you can make it do what it is supposed to do, you would simply run the accompanying SED-ML document and see the figures reproduced.


As with any new standards initiative, it will only be taken up if there are computational resources, that make it easy to use, and of course if the standard can be helpful. Currently, with SED-ML in a very early stage it is already possible to exchange time course simulation experiments, but not much more. However, it could be extended easily, such as by using a Nested Simulation Experiment, as described at the link below.

But what about computational resources? As it so happens, I’ve created a new project:

LibSedML - 

There, I provide three libraries:

  • LibSedML – a .NET library for reading and writing SED-ML
  • LibSedMLRunner  – a library on top of LibSedML, that schedules and runs simulation experiments.
  • LibSedMLScript – a utility library, turning a human readable script format into SED-ML.

Three applications support these libraries so far:

  • SED-ML Script: This application provides an easy way to define new Simulation Experiments using the human readable script format. No more struggling with API calls or XML, a simple script defines a simulation experiment. It can also be readily tested right then and there.
  • A web application provides the same functionality and provides a test bed, without having to download any software.
  • A plug-in for the SBW Simulation Tool, allows to run SED-ML files directly from it and provides capabilities for saving simple simulation experiments. (screenshot at beginning of this post)

The libraries and tools have been implemented using .NET, and have been confirmed to run fine on Windows, Linux and OS X!


Bergmann, Frank. A Simple Nested Simulation for SED-ML. Available from Nature Precedings <> (2010)

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