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See detailGeneCrunch: Experiences on the SGI POWER CHALLENGEarray with Bioinformatics applications
Schneider, Reinhard UL; Casari, G.; Daruvar, A. et al

in Supercomputer 96: Anwendungen, Architekturen, Trends (1996)

Analyzing genomic data is a computationally intensive and complicated process in which scientists must typically choose among multiple databases and analysis methods and make expert judgements inspecting ... [more ▼]

Analyzing genomic data is a computationally intensive and complicated process in which scientists must typically choose among multiple databases and analysis methods and make expert judgements inspecting multiple results. GeneQuiz, an automated software system for large scale genome analysis developed at the EMBL/EBI, tackles this problem by using an automated, rigorous, rule-based system to select among the results of sequence analysis and database searches, builds informative annotation and aims at predicting the function of new genes. In a demonstration project more than 6000 proteins from the Baker’s yeast, for which the complete genomic sequence was completed in 1996, were analyzed on a Silicon Graphics POWERCHALLENGEarray with 64 processors (R8000 @90 MHz) so that the analysis could be completed in 3 days. The results of the analysis were published on two web servers as they were computed. [less ▲]

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See detailGeneCrunch and Europort, examples for Hierarchical Supercomputing at Silicon Graphics
Schneider, Reinhard UL; Schlenkrich, M.

in WWW-publication (1996)

The SGI POWER CHALLENGEarray TM represents a hierarchical supercomputer because it combines distributed and shared memory technology. We present two projects, Europort and GeneCrunch, that took advantage ... [more ▼]

The SGI POWER CHALLENGEarray TM represents a hierarchical supercomputer because it combines distributed and shared memory technology. We present two projects, Europort and GeneCrunch, that took advantage of such a configuration. In Europort we performed scalability demonstrations up to 64 processors with applications relevant to the chemical and pharmaceutical industries. GeneCrunch, a project in bioinformatics, performed an analysis of the whole yeast genome using the software system GeneQuiz. This project showcased the future demands of HPC in pharmaceutical industries in tackling analysis of fast growing volumes of sequence information. GeneQuiz, an automated software system for large-scale genome analysis developed at the EMBL /EBI , aims at predicting the function of new genes by using an automated, rigorous, rule-based system to process the results of sequence analysis and database searches to build databases of annotations and predictions. In GeneCrunch more than 6,000 proteins from baker's yeast, for which the complete genomic sequence was completed in 1996, were analyzed on a SGI® POWER CHALLENGEarray with 64 processors (R8000® at 90MHz) in three days rather than the seven months predicted for a normal workstation [less ▲]

Detailed reference viewed: 88 (0 UL)