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SPRINT: A new parallel framework for R

Jon Hill1*, Matthew Hambley1, Thorsten Forster2, Muriel Mewissen2, Terence M Sloan1, Florian Scharinger1, Arthur Trew1 and Peter Ghazal2

Author Affiliations

1 EPCC, The University of Edinburgh, James Clerk Maxwell Building, Mayfield Road, Edinburgh, EH9 3JZ, UK

2 Division of Pathway Medicine (DPM), The University of Edinburgh Medical School, Chancellor's building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK

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BMC Bioinformatics 2008, 9:558  doi:10.1186/1471-2105-9-558

Published: 29 December 2008

Abstract

Background

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.

Results

We have designed and built a prototype framework that allows the addition of parallelised functions to R to enable the easy exploitation of HPC systems. The Simple Parallel R INTerface (SPRINT) is a wrapper around such parallelised functions. Their use requires very little modification to existing sequential R scripts and no expertise in parallel computing. As an example we created a function that carries out the computation of a pairwise calculated correlation matrix. This performs well with SPRINT. When executed using SPRINT on an HPC resource of eight processors this computation reduces by more than three times the time R takes to complete it on one processor.

Conclusion

SPRINT allows the biostatistician to concentrate on the research problems rather than the computation, while still allowing exploitation of HPC systems. It is easy to use and with further development will become more useful as more functions are added to the framework.