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GMB: An Efficient Query Processor for Biological Data

Taha, Kamal ; Elmasri, Ramez

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
Bioinformatics applications manage complex biological data stored into distributed and often heterogeneous databases and require large computing power. These databases are too big and complicated to be rapidly queried every time a user submits a query, due to the overhead involved in decomposing the queries, sending the decomposed queries to remote databases, and composing the results. There is also considerable communication costs involved. This study addresses the mentioned problems in Grid-based environment for bioinformatics. We propose a Grid middleware called GMB that alleviates these problems by caching the results of Frequently Used Queries (FUQ). Queries are classified based on their types and frequencies. FUQ are answered from the middleware, which improves their response time. GMB acts as a gateway to TeraGrid Grid: it resides between users' applications and TeraGrid Grid. We evaluate GMB experimentally.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
GMB: An Efficient Query Processor for Biological Data. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 8(2), 2011

Online-Journal: http://journal.imbio.de/article.php?aid=165
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2011/5181



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