GMB: An Efficient Query Processor for Biological Data

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doi doi:10.2390/biecoll-jib-2011-165
submission April 28, 2011
last revision July 22, 2011
published August 31, 2011
NCBI PubMed PubMed ID 21881166

Kamal Taha and Ramez Elmasri

Correspondence should be addressed to:
Kamal Taha
Khalifa University of Science, Technology & Research, Box 127788, Abu Dhabi, UAE
ea.ca.ratsuk@nullahat.lamak


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.

Reference

Kamal Taha and Ramez Elmasri. GMB: An Efficient Query Processor for Biological Data. Journal of Integrative Bioinformatics, 8(2):165, 2011. Online Journal: http://journal.imbio.de/index.php?paper_id=165
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