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. Categories and Subject Descriptors

• Type: Conference
• Year: 2010
• Where: HPDC
• Authors: Savvas Petrou, Terence M. Sloan, Muriel Mewissen, Thorsten Forster, Michal Piotrowski, Bartosz Dobrzelecki
• Keywords: Bioconductor Package, Bioinformatics Computing Infrastructures, Distributed And Parallel Computing, HPDC 2010, Permutation Testing Function