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Architectural Refactoring for Fast and Modular Bioinformatics Sequence Search

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dc.contributor.authorArchuleta, Jeremyen
dc.contributor.authorTilevich, Elien
dc.contributor.authorFeng, Wu-chunen
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2013-06-19T14:35:45Zen
dc.date.available2013-06-19T14:35:45Zen
dc.date.issued2006-09-01en
dc.description.abstractBioinformaticists use the Basic Local Alignment Search Tool (BLAST) to characterize an unknown sequence by comparing it against a database of known sequences, thus detecting evolutionary relationships and biological properties. mpiBLAST is a widely-used, high-performance, open-source parallelization of BLAST that runs on a computer cluster delivering super-linear speedups. However, the Achilles heel of mpiBLAST is its lack of modularity, adversely affecting maintainability and extensibility; an effective architectural refactoring will benefit both users and developers. This paper describes our experiences in the architectural refactoring of mpiBLAST into a modular, high-performance software package. Our evaluation of five component-oriented designs culminated in a design that enables modularity while retaining high-performance. Furthermore, we achieved this refactoring effectively and efficiently using eXtreme Programming techniques. These experiences will be of value to software engineers faced with the challenge of creating maintainable and extensible, high-performance, bioinformatics software.en
dc.format.mimetypeapplication/pdfen
dc.identifierhttp://eprints.cs.vt.edu/archive/00000924/en
dc.identifier.sourceurlhttp://eprints.cs.vt.edu/archive/00000924/01/mpiblast-icse07.pdfen
dc.identifier.trnumberTR-06-20en
dc.identifier.urihttp://hdl.handle.net/10919/19544en
dc.language.isoenen
dc.publisherDepartment of Computer Science, Virginia Polytechnic Institute & State Universityen
dc.relation.ispartofComputer Science Technical Reportsen
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectParallel computationen
dc.subjectDistributed computingen
dc.subjectBioinformaticsen
dc.subjectSoftware engineeringen
dc.titleArchitectural Refactoring for Fast and Modular Bioinformatics Sequence Searchen
dc.typeTechnical reporten
dc.type.dcmitypeTexten

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