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Thursday, April 29, 2010

RoadRunner & Java (!?)

Darren Wilkinson is here this week early for the Hackathon this weekend. One of his projects is CaliBayes, which addresses the issue of estimating  parameters of kinetic laws. CaliBayes uses Java, and until now using RoadRunner required to go through the SBW Java bindings, to the SBW Broker to RoadRunner. It seems apparent, that this won’t deliver the best possible performance.

A couple of weeks ago I first dabbled in embedding the mono runtime for use of RoadRunner in C++. So it seemed clear, that this could be extended to the JNI world.

A prototype was quickly written and tested on OSX (10.6, using a 32bit JVM) and verified to work on Ubuntu 9.10 (32 bit). So far the version is not working in 64bit Linux. Mainly because all our libraries are not yet available for 64bit. Oh well … but it is a start …

The Ubuntu version is now online on the source forge project, source code an all:

Wednesday, April 28, 2010

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:

BioModel 140: