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-Watermanand 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.
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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: Dubitzky, W., Schuster, A., Sloot, P.M.A., Schroeder, M., Romberg, M. (eds) Distributed, High-Performance and Grid Computing in Computational Biology. GCCB 2007. Lecture Notes in Computer Science(), vol 4360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69968-2_2
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DOI: https://doi.org/10.1007/978-3-540-69968-2_2
Publisher Name: Springer, Berlin, Heidelberg
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