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Bioinformatics Advance Access published online on September 23, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti034
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received January 4, 2004
Revised August 16, 2004
Accepted September 10, 2004

Article

GLAD: a system for developing and deploying large-scale bioinformatics grid

Yong-Meng TEO 1*, Xianbing Wang 1, and Yew-Kwong NG 2

1 Department of Computer Science, National University of Singapore, Singapore 117543; Singapore-MIT Alliance, Singapore 117576
2 Department of Computer Science, National University of Singapore, Singapore 117543

* To whom correspondence should be addressed. E-mail: teoym{at}comp.nus.edu.sg.


  Abstract

Motivation: Grid computing is used to solve large-scale bioinformatics problem with gigabytes database by distributing the computation across multiple platforms. But up to now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems, and to access remotely located sequence database files of varying formats across the grid. Herein, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), to facilitate the development and deployment of bioinformatics applications on a grid.

Results: GLAD has been developed using ALiCE (Adaptive scaLable Internet-based Computing Engine), a Java-based grid middleware, which exploits task-based parallelism. Two bioinformatics benchmark applications, distributed sequence comparison and distributed progressive multiple sequence alignment, have been developed using GLAD.

Availability: GLAD and ALiCE are available at http://www.comp.nus.edu.sg/~teoym/alice.htm.


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