Designing Efficient Java Communications on Clusters
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 5 - Volume 06
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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-likemessage-passing and collective communication to the genomics Research Network Architecture (gRNA). The parallel implementation leads to significant runtime savings on our distributed gRNA system.