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Applications of grid computing in genetics and proteomics
KTH, School of Biotechnology (BIO), Gene Technology.
KTH, School of Biotechnology (BIO), Gene Technology.
KTH, School of Biotechnology (BIO), Proteomics.
KTH, School of Biotechnology (BIO), Gene Technology.ORCID iD: 0000-0003-0996-1644
2007 (English)In: Applied Parallel Computing: State Of The Art In Scientific Computing / [ed] Kagstrom, B; Elmroth, E; Dongarra, J; Wasniewski, J, 2007, Vol. 4699, 791-798 p.Conference paper, Published paper (Refereed)
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.

Place, publisher, year, edition, pages
2007. Vol. 4699, 791-798 p.
Series
Lecture Notes in Computer Science, ISSN 0302-9743 ; 4699
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-41136ISI: 000250904900096Scopus ID: 2-s2.0-38049037014ISBN: 978-3-540-75754-2 (print)OAI: oai:DiVA.org:kth-41136DiVA: diva2:443514
Conference
8th International Workshop on Applied Parallel Computing (PARA 2006) Location: Umea, Sweden, Date: JUN 18-21, 2006
Available from: 2011-09-26 Created: 2011-09-23 Last updated: 2012-03-20Bibliographically approved

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CiteExportLink to record
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Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
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  • de-DE
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  • nn-NB
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  • Other locale
More languages
Output format
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  • asciidoc
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