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Sunday, June 10, 2012

SED-ML Nested Proposal V3

A new version of the nested proposal is available immediately from:

The new version rephrases the Nested Simulation Class as Repeated Task, and addresses comments made by the community over the past couple of months (and of course the discussions at HARMONY 2012). As far as the scope is concerned, the current proposal is capable of describing all experiments possible with the previous version. Additionally through a new listOfSubTasks additional experiments can be run.

Steady state scan image
Pulsing a parameter during a simulation image
Multiple Stochastic Traces image
Timecourse scan image
2D Steady State scan image


Of course there also is an implementation available in the SED-ML Web Tools, where all examples can be run directly.

Friday, June 8, 2012

SBML Spatial Extension & Simulation

As part of my new job at the University of Heidelberg I get to work again on spatial simulations. While trying to get my feet wet, I was able to experiment with a spatial simulator by Akira Funahasi’s group (see also his presentation at last years COMBINE). So today I just wanted to share the resulting video with you:

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It always is fascinating watching these things. And the real amazing thing is that this is not a hard coded simulation, but one that is interpreted from an SBML file. And while it probably will take a while until we are regularly exchanging spatial models we are definitely on the right way!