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dc.contributor.authorArchuleta, Jeremyen_US
dc.contributor.authorTilevich, Elien_US
dc.contributor.authorFeng, Wu-chunen_US
dc.date.accessioned2013-06-19T14:35:45Z
dc.date.available2013-06-19T14:35:45Z
dc.date.issued2006-09-01
dc.identifierhttp://eprints.cs.vt.edu/archive/00000924/en_US
dc.identifier.urihttp://hdl.handle.net/10919/19544
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_US
dc.format.mimetypeapplication/pdfen_US
dc.publisherDepartment of Computer Science, Virginia Polytechnic Institute & State Universityen_US
dc.relation.ispartofComputer Science Technical Reportsen_US
dc.subjectParallel computationen_US
dc.subjectDistributed computingen_US
dc.subjectBioinformaticsen_US
dc.subjectSoftware engineeringen_US
dc.titleArchitectural Refactoring for Fast and Modular Bioinformatics Sequence Searchen_US
dc.typeTechnical reporten_US
dc.identifier.trnumberTR-06-20en_US
dc.type.dcmitypeTexten_US
dc.identifier.sourceurlhttp://eprints.cs.vt.edu/archive/00000924/01/mpiblast-icse07.pdf


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