Grid-based data access to nucleotide sequence database

Frank Wang; Sining Wu; Na Helian; zhiwei Xu; Yuhui Deng; Vineet Khare; Chenhan Liao; Chris Thompson; Michael Andrew Parker

doi:10.1007/s00354-007-0026-4

Grid-based data access to nucleotide sequence database

Frank Wang, Sining Wu, Na Helian, zhiwei Xu, Yuhui Deng, Vineet Khare, Chenhan Liao, Chris Thompson, Michael Andrew Parker

Research output: Contribution to journal › Article › peer-review

Abstract

The International Nucleotide Sequence Database Collaboration (INSDC) exchanges sequence data on a daily basis across its three member organizations in the USA, UK and Japan. This paper studies how this sequence database in MySQL can best take advantage of the increased transfer bandwidth of a Grid-optimized data communication protocol. Within the context of the UK Government Project Grid-oriented Storage (GOS) and the EC Project EuroAsiaGrid, GOS File System (GOS-FS) has been developed in our lab, which melds distributed file system technology with high performance data transfer techniques to meet the needs of WAN/Grid-based virtual organizations. A real-world test shows that the INSDC sequence database backing up operation, mysqldump, over the GOS-FS protocol beats those over the classic NFS protocol by 6 times over the link between Cambridge and Tokyo. Best of all, the …

Original language	English
Pages (from-to)	409-424
Journal	New Generation Computing
DOIs	https://doi.org/10.1007/s00354-007-0026-4
Publication status	Published - Aug 2007

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AU - Wang, Frank

AU - Wu, Sining

AU - Helian, Na

AU - Xu, zhiwei

AU - Deng, Yuhui

AU - Khare, Vineet

AU - Liao, Chenhan

AU - Thompson, Chris

AU - Parker, Michael Andrew

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Grid-based data access to nucleotide sequence database

Abstract

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