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SPRINT: a new parallel framework for R

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http://www.biomedcentral.com/1471-2105/9/558
Original languageEnglish
Pages (from-to)558
JournalBMC Bioinformatics
Volume9
DOIs
StatePublished - 2008

Abstract

Microarray analysis allows the simultaneous measurement of thousands to millions of genes or sequences across tens to thousands of different samples. The analysis of the resulting data tests the limits of existing bioinformatics computing infrastructure. A solution to this issue is to use High Performance Computing (HPC) systems, which contain many processors and more memory than desktop computer systems. Many biostatisticians use R to process the data gleaned from microarray analysis and there is even a dedicated group of packages, Bioconductor, for this purpose. However, to exploit HPC systems, R must be able to utilise the multiple processors available on these systems. There are existing modules that enable R to use multiple processors, but these are either difficult to use for the HPC novice or cannot be used to solve certain classes of problems. A method of exploiting HPC systems, using R, but without recourse to mastering parallel programming paradigms is therefore necessary to analyse genomic data to its fullest.

    Research areas

  • Algorithms, Animals, Computational Biology, Computer Graphics, Computing Methodologies, Databases, Genetic, Gene Expression Profiling, Genomics, Humans, Oligonucleotide Array Sequence Analysis, Pattern Recognition, Automated, Programming Languages, Software, User-Computer Interface

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