The role of parallel computing in bioinformatics

Akhurst, Timothy John (2005) The role of parallel computing in bioinformatics. Masters thesis, Rhodes University.




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.

Item Type:Thesis (Masters)
Additional Information:Research report submitted in partial fulfilment of the requirements for the degree of Master of Science
Uncontrolled Keywords:Bioinformatics, parallel programming, LINDA (Computer system), Java programming language, parallel processing, genomics
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions:Faculty > Faculty of Science > Computer Science
Faculty > Faculty of Science > Biochemistry, Microbiology & Biotechnology
Supervisors:Wells, G.C. (Prof.)
ID Code:162
Deposited By: Rhodes Library Archive Administrator
Deposited On:16 Nov 2005
Last Modified:06 Jan 2012 16:17
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