NDLI: RE-PAGE: Domain-Specific REplication and PArallel Processing of GEnomic Data

Content Provider	IEEE Xplore Digital Library
Author	Kutlu, M. Agrawal, G.
Copyright Year	2015
Description	Author affiliation: Dept. of Comput. Sci. & Eng., Ohio State Univ., Columbus, OH, USA (Kutlu, M.; Agrawal, G.)
Abstract	As development of high-throughput and low-cost sequencing technologies is leading to massive volumes of genomic data, new solutions for handling data-intensive applications on parallel platforms are urgently required. Particularly, the nature of processing leads to both load balancing and I/O contention challenges. In this paper, we have developed a novel middleware system, RE-PAGE, which allows parallelization of applications that process genomic data with a simple, high-level API. To address load balancing and I/O contention, the features of the middleware include: 1) use of domain-specific information in the formation of data chunks (which can be of non-uniform sizes), 2) replication and placement of each chunk on a small number of nodes, performed in an intelligent way, and 3) scheduling schemes for achieving load balance, when data movement costs out-weigh processing costs and the chunks are of non-uniform sizes. We have evaluated our framework using three genomic applications, which are VarScan, Unified Genotyper, and Coverage Analyzer. We show that our approach leads to better performance than conventional MapReduce scheduling approaches and systems that access data from a centralized store. We also compare against popular frameworks, Hadoop and GATK, and show that our middleware outperforms both, achieving high parallel efficiency and scalability.
Starting Page	332
Ending Page	341
File Size	384773
Page Count	10
File Format	PDF
ISBN	9781467365987
DOI	10.1109/CLUSTER.2015.54
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2015-09-08
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Genomics Bioinformatics Middleware Load management Processor scheduling Sequential analysis Genomic Applications Parallel Computing Middleware Systems
Content Type	Text
Resource Type	Article

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