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Applications of grid computing in genetics and proteomics
KTH, Skolan för bioteknologi (BIO), Genteknologi.
KTH, Skolan för bioteknologi (BIO), Genteknologi.
KTH, Skolan för bioteknologi (BIO), Proteomik.
KTH, Skolan för bioteknologi (BIO), Genteknologi.ORCID-id: 0000-0003-0996-1644
2007 (engelsk)Inngår i: Applied Parallel Computing: State Of The Art In Scientific Computing / [ed] Kagstrom, B; Elmroth, E; Dongarra, J; Wasniewski, J, 2007, Vol. 4699, s. 791-798Konferansepaper, Publicerat paper (Fagfellevurdert)
Abstract [en]

The potential for Grid technologies in applied bioinformatics is largely unexplored. We have developed a model for solving computationally demanding bioinformatics tasks in distributed Grid environments, designed to ease the usability for scientists unfamiliar with Grid computing. With a script-based implementation that uses a strategy of temporary installations of databases and existing executables on remote nodes at submission, we propose a generic solution that do not rely on predefined Grid runtime environments and that can easily be adapted to other bioinformatics tasks suitable for parallelization. This implementation has been successfully applied to whole proteome sequence similarity analyses and to genome-wide genotype simulations, where computation time was reduced from years to weeks. We conclude that computational Grid technology is a useful resource for solving high compute tasks in genetics and proteomics using existing algorithms.

sted, utgiver, år, opplag, sider
2007. Vol. 4699, s. 791-798
Serie
Lecture Notes in Computer Science, ISSN 0302-9743 ; 4699
HSV kategori
Identifikatorer
URN: urn:nbn:se:kth:diva-41136ISI: 000250904900096Scopus ID: 2-s2.0-38049037014ISBN: 978-3-540-75754-2 (tryckt)OAI: oai:DiVA.org:kth-41136DiVA, id: diva2:443514
Konferanse
8th International Workshop on Applied Parallel Computing (PARA 2006) Location: Umea, Sweden, Date: JUN 18-21, 2006
Tilgjengelig fra: 2011-09-26 Laget: 2011-09-23 Sist oppdatert: 2018-01-12bibliografisk kontrollert

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