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International Parallel and Distributed Processing Symposium (IPDPS'03)   p. 156b
Parallel Detection of Regulatory Elements with gMP
Bertil Schmidt, Nanyang Technological University
Lin Feng, Nanyang Technological University
Amey Laud, Helixense Pte Ltd
Yusdi Santoso, Helixense Pte Ltd

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DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/IPDPS.2003.1213294
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Abstract
The detection of regulatory elements from a large set of regulatory regions is a challenging problem in computational genomics. However, computational methods to extract this biological meaningful information suffer from high computational requirements. In this paper we present a parallel algorithm to detect regulatory elements using correlation with gene expression data and its implementation with gMP. gMP is a new purely Java-based interface that adds MPI-like message-passing and collective communication to the genomics Research Network Architecture (gRNA). The parallel implementation leads to significant runtime savings on our distributed gRNA system.
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Citation:  Bertil Schmidt, Lin Feng, Amey Laud, Yusdi Santoso, "Parallel Detection of Regulatory Elements with gMP," ipdps, p. 156b,  International Parallel and Distributed Processing Symposium (IPDPS'03),  2003