DocumentCode :
3190290
Title :
A lightweight, scalable grid computing framework for parallel bioinformatics applications
Author :
De Sterck, Hans ; Markel, Rob ; Knight, Rob
Author_Institution :
Dept. of Appl. Math., Waterloo Univ., Ont., Canada
fYear :
2005
fDate :
15-18 May 2005
Firstpage :
251
Lastpage :
257
Abstract :
In recent years our society has witnessed an unprecedented growth in computing power available to tackle important problems in science, engineering and medicine. For example, the SHARCNET network links large computing resources in 11 leading academic institutions in South Central Ontario, thus providing access to thousands of compute processors. It is a continuous challenge to develop efficient and scalable algorithms and methods for solving large scientific and engineering problems on such parallel and distributed computers. If the computing power available in such computational grids can be unleashed effectively in a scalable way, large scientific problems can be solved that would otherwise be hard to solve using the machines available in a stand-alone way. This paper describes techniques and software developed that allow to apply the power of computational grids to large-scale, loosely coupled parallel bioinformatics problems. Our approach is based on decentralization and implemented in Java, leading to a flexible, portable and scalable software solution for parallel bioinformatics. We discuss advantages and disadvantages of this approach, and demonstrate seamless performance on an ad-hoc grid composed of a wide variety of hardware for a real-life parallel bioinformatics problem. The bioinformatics problem described consists of virtual experiments in RNA folding executed on hundreds of compute processors concurrently, which may establish one of the missing links in the chain events that led to the origin of life.
Keywords :
biology computing; grid computing; macromolecules; Java; RNA; ad-hoc grid; grid computing; loosely coupled parallel bioinformatics; Bioinformatics; Computer networks; Concurrent computing; Distributed computing; Grid computing; Hardware; Java; Large-scale systems; Power engineering and energy; Power engineering computing;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
High Performance Computing Systems and Applications, 2005. HPCS 2005. 19th International Symposium on
ISSN :
1550-5243
Print_ISBN :
0-7695-2343-9
Type :
conf
DOI :
10.1109/HPCS.2005.7
Filename :
1430079
Link To Document :
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