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The automated annotation of data from high throughput sequencing and genomics experiments is a significant challenge for bioinformatics. Most current approaches rely on sequential pipelines of gene finding and gene function prediction methods that annotate a gene with information from different reference data sources. Each function prediction method contributes evidence supporting a functional assignment. Such approaches generally ignore the links between the information in the reference datasets. These links, however, are valuable for assessing the plausibility of a function assignment and can be used to evaluate the confidence in a prediction. We are working towards a novel annotation system that uses the network of information supporting the function assignment to enrich the annotation process for use by expert curators and predicting the function of previously unannotated genes. In this paper we describe our success in the first stages of this development. We present the data integration steps that are needed to create the core database of integrated reference databases (UniProt, PFAM, PDB, GO and the pathway database Ara-Cyc) which has been established in the ONDEX data integration system. We also present a comparison between different methods for integration of GO terms as part of the function assignment pipeline and discuss the consequences of this analysis for improving the accuracy of gene function annotation. The methods and algorithms presented in this publication are an integral part of the ONDEX system which is freely available from http://ondex.sf.net/.
The Render Cache [1,2] allows the interactive display of very large scenes, rendered with complex global illumination models, by decoupling camera movement from the costly scene sampling process. In this paper, the distributed execution of the individual components of the Render Cache on a PC cluster is shown to be a viable alternative to the shared memory implementation.As the processing power of an entire node can be dedicated to a single component, more advanced algorithms may be examined. Modular functional units also lead to increased flexibility, useful in research as well as industrial applications.We introduce a new strategy for view-driven scene sampling, as well as support for multiple camera viewpoints generated from the same cache. Stereo display and a CAVE multi-camera setup have been implemented.The use of the highly portable and inter-operable CORBA networking API simplifies the integration of most existing pixel-based renderers. So far, three renderers (C++ and Java) have been adapted to function within our framework.