Using public resource computing and systematic pre-calculation for large scale sequence analysis

Thomas Rattei; Mathias Walter; Roland Arnold; David P. Anderson; Werner Mewes

doi:10.1007/978-3-540-69968-2_2

Using public resource computing and systematic pre-calculation for large scale sequence analysis

Thomas Rattei
, Mathias Walter
, Roland Arnold
, David P. Anderson
, Werner Mewes

Life Sciences

Technical University of Munich
Helmholtz Zentrum München German Research Center for Environmental Health
Space Sciences Laboratory at UC Berkeley

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

4 Scopus citations

Abstract

High volumes of serial computational tasks in bioinformatics, such as homology searches or profile matching, are often executed in distributed environments using classical batching systems like LSF or Sun Grid-Engine. Despite their simple usability they are limited to organizationally owned resources. In contrast to proprietary projects that implement large-scale grids we report on a grid-enabled solution for sequence homology and protein domain searches using BOINC, the Berkeley Open Infrastructure for Network Computing. We demonstrate that BOINC provides a powerful and versatile platform for public resource computing in bioinformatics that makes large-scale pre-calculation of sequence analyses feasible. The FASTA-/Smith-Waterman-and HMMer applications for BOINC are freely available from the authors upon request. Data from SIMAP is publicly available through Web-Services at http://mips.gsf.de/simap.

Original language	English
Title of host publication	Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings
Publisher	Springer Verlag
Pages	11-18
Number of pages	8
ISBN (Print)	3540698418, 9783540698418
DOIs	https://doi.org/10.1007/978-3-540-69968-2_2
State	Published - 2007
Event	Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006 - Eilat, Israel Duration: 21 Jan 2007 → 21 Jan 2007

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4360 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006
Country/Territory	Israel
City	Eilat
Period	21/01/07 → 21/01/07

Keywords

Grid computing
Protein domain
Protein homology
Public resource computing
Sequence analysis
Sequence similarity

Access to Document

10.1007/978-3-540-69968-2_2

Cite this

Rattei, T., Walter, M., Arnold, R., Anderson, D. P., & Mewes, W. (2007). Using public resource computing and systematic pre-calculation for large scale sequence analysis. In Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings (pp. 11-18). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4360 LNBI). Springer Verlag. https://doi.org/10.1007/978-3-540-69968-2_2

Rattei, Thomas ; Walter, Mathias ; Arnold, Roland et al. / Using public resource computing and systematic pre-calculation for large scale sequence analysis. Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings. Springer Verlag, 2007. pp. 11-18 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "High volumes of serial computational tasks in bioinformatics, such as homology searches or profile matching, are often executed in distributed environments using classical batching systems like LSF or Sun Grid-Engine. Despite their simple usability they are limited to organizationally owned resources. In contrast to proprietary projects that implement large-scale grids we report on a grid-enabled solution for sequence homology and protein domain searches using BOINC, the Berkeley Open Infrastructure for Network Computing. We demonstrate that BOINC provides a powerful and versatile platform for public resource computing in bioinformatics that makes large-scale pre-calculation of sequence analyses feasible. The FASTA-/Smith-Waterman-and HMMer applications for BOINC are freely available from the authors upon request. Data from SIMAP is publicly available through Web-Services at http://mips.gsf.de/simap.",

keywords = "Grid computing, Protein domain, Protein homology, Public resource computing, Sequence analysis, Sequence similarity",

author = "Thomas Rattei and Mathias Walter and Roland Arnold and Anderson, \{David P.\} and Werner Mewes",

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publisher = "Springer Verlag",

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booktitle = "Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings",

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Rattei, T, Walter, M, Arnold, R, Anderson, DP & Mewes, W 2007, Using public resource computing and systematic pre-calculation for large scale sequence analysis. in Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4360 LNBI, Springer Verlag, pp. 11-18, Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Eilat, Israel, 21/01/07. https://doi.org/10.1007/978-3-540-69968-2_2

Using public resource computing and systematic pre-calculation for large scale sequence analysis. / Rattei, Thomas; Walter, Mathias; Arnold, Roland et al.
Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings. Springer Verlag, 2007. p. 11-18 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4360 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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T1 - Using public resource computing and systematic pre-calculation for large scale sequence analysis

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AU - Walter, Mathias

AU - Arnold, Roland

AU - Anderson, David P.

AU - Mewes, Werner

PY - 2007

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N2 - High volumes of serial computational tasks in bioinformatics, such as homology searches or profile matching, are often executed in distributed environments using classical batching systems like LSF or Sun Grid-Engine. Despite their simple usability they are limited to organizationally owned resources. In contrast to proprietary projects that implement large-scale grids we report on a grid-enabled solution for sequence homology and protein domain searches using BOINC, the Berkeley Open Infrastructure for Network Computing. We demonstrate that BOINC provides a powerful and versatile platform for public resource computing in bioinformatics that makes large-scale pre-calculation of sequence analyses feasible. The FASTA-/Smith-Waterman-and HMMer applications for BOINC are freely available from the authors upon request. Data from SIMAP is publicly available through Web-Services at http://mips.gsf.de/simap.

AB - High volumes of serial computational tasks in bioinformatics, such as homology searches or profile matching, are often executed in distributed environments using classical batching systems like LSF or Sun Grid-Engine. Despite their simple usability they are limited to organizationally owned resources. In contrast to proprietary projects that implement large-scale grids we report on a grid-enabled solution for sequence homology and protein domain searches using BOINC, the Berkeley Open Infrastructure for Network Computing. We demonstrate that BOINC provides a powerful and versatile platform for public resource computing in bioinformatics that makes large-scale pre-calculation of sequence analyses feasible. The FASTA-/Smith-Waterman-and HMMer applications for BOINC are freely available from the authors upon request. Data from SIMAP is publicly available through Web-Services at http://mips.gsf.de/simap.

KW - Grid computing

KW - Protein domain

KW - Protein homology

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KW - Sequence analysis

KW - Sequence similarity

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T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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ER -

Rattei T, Walter M, Arnold R, Anderson DP, Mewes W. Using public resource computing and systematic pre-calculation for large scale sequence analysis. In Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings. Springer Verlag. 2007. p. 11-18. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-69968-2_2

Using public resource computing and systematic pre-calculation for large scale sequence analysis

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Keywords

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