International Conference on Systems Biology, Edinburgh, 10-14th Oct 2010

ICSB is a bioinformatics conference with a focus on system models. On Monday I attended a talk on SBML model merging, by Francois Fages, Inria. Fages presented a method for model merging and hierarchy building that is based on constraint programming. The source data were from biomodels.org, and the method used four merging primitives: species deletion, reaction deletion, species merging, and reaction merging. For more information see http://gprolog.inria.fr and http://contraintes.inria.fr. The approach is purely structural and does not work for larger models (due to time out).

I presented a SyBIT poster on Monday. This gives an overview of our work, with stress on workflows  driven by PGRADE and iBRAIN2, and openBIS database. Several UK and German groups expressed interest in the software and its portability.

On Tuesday Tom Freeman from Roslyn Institute spoke on BioLayoutExpress, http://www.biolayout.org. The software supports 3D visualisation and detailed analysis of expression data. It allows one to cluster a dataset or two datasets and examine the results of the clustering. This provides a method for data integration.

On Wednesday Richard Baldock (MRC HGU Edinburgh) gave a very interesting talk on bioatlasses. He gave examples for the mouse brain atlas, where 3D images are annotated manually, with reference to an ontology of anatomical terms. Christian von Mering gave a talk about protein interactions – relationships between protein (MS) measured abundance and expression and protein abundance in various species (stored in pax-db).

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