Construct a grid computing environment for bioinformatics

Kuo, Yu-Lun; Yang, Chao‐Tung; Lai, Chuan-Lin; Tseng, Tsai-Ming

doi:10.1109/ispan.2004.1300502

Cited by 4 publications

References 10 publications

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HGBS: a hardware-oriented grid BLAST system

Kim

Lee

et al. 2005

CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.

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BLAST is one of the most widely used tools in bioinformatics to find biologically similar sequences from the genome databases for a given query sequence. Although elaborate dynamic programming and heuristic search in the BLAST rapidly identify significant similar sequences, performance is still an important issue as the size of genome databases. and sequences to be compared increases. We propose HGBS (Hardware-Oriented Grid BLAST System) that significantly improves the BLAST performance by applying the grid computing technique. HGBS utilizes a PC-based grid environment constructed by a specialized hardware chip, not a grid middleware such as the Globus toolkit, to provide enhanced performance, good extensibility, and lower implementation cost. Performance analysis shows that there is a significant performance advantage in HGBS;for huge number of BLAST operations in 89prokaryote genomes comparison, HGBS connecting 27 PCs needs just a week to complete the comparisons, but a single server system takes about 33 weeks.

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HGBS: a hardware-oriented grid BLAST system

Kim

Lee

et al. 2005

CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.

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A LanLinux-based grid system for bioinformatics applications

Kim

Oh²,

Cho³

2006

2006 8th International Conference Advanced Communication Technology

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Assemble Worldwide Biologists in a Network Construct a Web Services Based Architecture for Bioinformatics

Tao

Liu

2005

2005 IEEE Engineering in Medicine and Biology 27th Annual Conference

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The Internet has already deflated our world of working and living into a very small scope, thus bringing out the concept of Earth Village, in which people could communicate and co-work though thousands' miles far away from each other. This paper describes a prototype, which is just like an Earth Lab for bioinformatics, based on Web services framework to build up a network architecture for bioinformatics research and for world wide biologists to easily implement enormous, complex processes, and effectively share and access computing resources and data, regardless of how heterogeneous the format of the data is and how decentralized and distributed these resources are around the world. A diminutive and simplified example scenario is given out to realize the prototype after that.

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Construct a grid computing environment for bioinformatics

Cited by 4 publications

References 10 publications

HGBS: a hardware-oriented grid BLAST system

HGBS: a hardware-oriented grid BLAST system

A LanLinux-based grid system for bioinformatics applications

Assemble Worldwide Biologists in a Network Construct a Web Services Based Architecture for Bioinformatics

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