Return to search

The role of parallel computing in bioinformatics

The need to intelligibly capture, manage and analyse the ever-increasing amount of publicly available genomic data is one of the challenges facing bioinformaticians today. Such analyses are in fact impractical using uniprocessor machines, which has led to an increasing reliance on clusters of commodity-priced computers. An existing network of cheap, commodity PCs was utilised as a single computational resource for parallel computing. The performance of the cluster was investigated using a whole genome-scanning program written in the Java programming language. The TSpaces framework, based on the Linda parallel programming model, was used to parallelise the application. Maximum speedup was achieved at between 30 and 50 processors, depending on the size of the genome being scanned. Together with this, the associated significant reductions in wall-clock time suggest that both parallel computing and Java have a significant role to play in the field of bioinformatics.

Identiferoai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:rhodes/vital:3986
Date January 2005
CreatorsAkhurst, Timothy John
PublisherRhodes University, Faculty of Science, Biochemistry, Microbiology and Biotechnology
Source SetsSouth African National ETD Portal
LanguageEnglish
Detected LanguageEnglish
TypeThesis, Masters, MSc
Formatxi, 78 leaves, pdf
RightsAkhurst, Timothy John

Page generated in 0.0019 seconds