论文信息 - Optimization of a parallel permutation testing function for the SPRINT R package

Optimization of a parallel permutation testing function for the SPRINT R package

The statistical language R and Bioconductor package are favoured by many biostatisticians for processing microarray data. The amount of data produced by these analyses has reached the limits of many common bioinformatics computing infrastructures. High Performance Computing (HPC) systems offer a solution to this issue. The Simple Parallel R INTerface (SPRINT) is a package that provides biostatisticians with easy access to HPC systems and allows the addition of parallelized functions to R. This paper will present how we added a parallelized permutation testing function in R using SPRINT and how this function performs on a supercomputer for executions of up to 512 processes.

[1] S. Dudoit,et al. Resampling-based multiple testing for microarray data analysis , 2003 .

[2] Jon Hill,et al. Optimization of a parallel permutation testing function for the SPRINT R package , 2011, Concurr. Comput. Pract. Exp..

[3] Message Passing Interface Forum. MPI: A message - passing interface standard , 1994 .

[4] S. S. Young,et al. Resampling-Based Multiple Testing: Examples and Methods for p-Value Adjustment , 1993 .

[5] Lawrence Mitchell,et al. A parallel random forest classifier for R , 2011, ECMLS '11.

[6] Neil P. Chue Hong,et al. Managing and Analysing Genomic Data Using HPC and Clouds , 2011, Grid and Cloud Database Management.

[7] Hao Yu,et al. State of the Art in Parallel Computing with R , 2009 .

[8] Andreas Polze,et al. Joint Forces: From Multithreaded Programming to GPU Computing , 2011, IEEE Software.

[9] Jon Hill,et al. SPRINT: A new parallel framework for R , 2008, BMC Bioinformatics.

[10] References , 1971 .

[11] Rolf Hempel,et al. The MPI Message Passing Interface Standard , 1994 .

[12] C. Pipper,et al. [''R"--project for statistical computing]. , 2008, Ugeskrift for laeger.