Parallelism in Bioinformatics Workflows

• Published in: High Performance Computing for Computational Science - VECPAR 2004 pp. 583 - 597
• Main Authors: Meyer, Luiz A. V. C., Rössle, Shaila C., Bisch, Paulo M., Mattoso, Marta
• Format: Book Chapter Conference Proceeding
• Language: English
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 2005; Springer
• Series: Lecture Notes in Computer Science
• Subjects: Applied sciences; Comparative Modeling Approach; Computer science; control theory; systems; Computer systems and distributed systems. User interface; Entry Sequence; Exact sciences and technology; Information systems. Data bases; Memory organisation. Data processing; Parallel Execution; Parallelism Strategy; Simultaneous Execution; Software; Groupware; High performance; Parallel processing; Data distribution; Parallelism; Workflow; Genome; Bioinformatics; Distributed computing; Database management system; Annotation
• ISBN: 9783540254249; 3540254242
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/11403937_44

Parallel processing is frequently used in bioinformatics programs and in Database Management Systems to improve their performance. Parallelism can be also used to improve performance of a combination of programs in bioinformatics workflows. This work presents a characterization of parallel processing in scientific workflows and shows real experimental results with different configurations for data and programs distribution within bioinformatics workflow execution. The implementation was done with real structural genomic and automatic comparative annotation workflows and the experiments run on a cluster of PCs.