A Maintainable Software Architecture for Fast and Modular Bioinformatics Sequence Search

Bioinformaticists 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, opensource parallelization of BLAST that runs on a computer cluster delivering super-linear speedups. However, the Achilles heel of mpiBLAST is its lack of modularity, thus adversely affecting maintainability and extensibility. Alleviating this shortcoming requires an architectural refactoring to improve maintenance and extensibility while preserving high performance. Toward that end, this paper evaluates five different software architectures and details how each satisfies our design objectives. In addition, we introduce a novel approach to using mixin layers to enable mixing-and-matching of modules in constructing sequence-search applications for a variety of high-performance computing systems. Our design, which w...

• Type: Conference
• Year: 2007
• Where: ICSM
• Authors: Jeremy S. Archuleta, Eli Tilevich, Wu-chun Feng
• Keywords: Basic Local Alignment Search Tool, ICSM 2007, Mixin Layers, Opensource Parallelization, Software Engineering