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See detailPedestrian guide to analyzing sequence databases
Rost, B.; Schneider, Reinhard UL; Sander, C.

in WWW-publication (1997)

Over the past few years our means of communication have changed rapidly due to the growth of the World Wide Web (WWW). The Web enables molecular biologists to immediately access databases, scan literature ... [more ▼]

Over the past few years our means of communication have changed rapidly due to the growth of the World Wide Web (WWW). The Web enables molecular biologists to immediately access databases, scan literature, find information about related research and researchers, and to trace cell cultures. Wet-lab biologists can uncover information about the protein of interest without having to become experts in sequence analysis. Here, we present a variety of tools; provide an overview of the state-of-the art in sequence analysis; and described some of the principles of the methods. [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 ▲]

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