DSIMBench: A Benchmark for Microarray Data Using R

Parallel computing in R has been widely used to analyse microarray data. We have seen various applications using various data distribution and calculation approaches. Newer data storage systems, such as MySQL Cluster and HBase, have been proposed for R data storage; while the parallel computation fr...

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Bibliographic Details
Published inBig Data Benchmarks, Performance Optimization, and Emerging Hardware pp. 47 - 56
Main Authors Wang, Shicai, Pandis, Ioannis, Emam, Ibrahim, Johnson, David, Guitton, Florian, Oehmichen, Axel, Guo, Yike
Format Book Chapter
LanguageEnglish
Published Cham Springer International Publishing 2014
SeriesLecture Notes in Computer Science
Subjects
Benchmark
MapReduce
MPI
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Summary:Parallel computing in R has been widely used to analyse microarray data. We have seen various applications using various data distribution and calculation approaches. Newer data storage systems, such as MySQL Cluster and HBase, have been proposed for R data storage; while the parallel computation frameworks, including MPI and MapReduce, have been applied to R computation. Thus, it is difficult to understand the whole analysis workflows for which the tool kits are suited for a specific environment. In this paper we propose DSIMBench, a benchmark containing two classic microarray analysis functions with eight different parallel R workflows, and evaluate the benchmark in the IC Cloud testbed platform.
ISBN:9783319130200
331913020X
ISSN:0302-9743
1611-3349
DOI:10.1007/978-3-319-13021-7_4