The Division of Pathway Medicine, (DPM) (http://www.pathwaymedicine.ed.ac.uk), is a multi-disciplinary centre for world class post-genomic research located within the University of Edinburgh Medical School. Over the past few years, the bioinformatics team at DPM has built a vast expertise in supporting microarray research including data production, data collection, data standards, data storage and data analysis. DPM biostatisticians are experts in applying the latest and most appropriate statistical methods and tools to a large range of microarray expression data. Presently, they have identified one constant limitation in their ability to successfully unlock scientific knowledge from the data available now; it is the presently unfulfilled need for an easy access to High Performance Computing (HPC).
As part of edikt2, EPCC and DPM 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), available from http://forge.nesc.ac.uk/projects/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.
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.
EPCC and DPM have successfully obtained further funding from the Wellcome Trust to prodcutise and extend SPRINT. More information is available on the SPRINT web site at http://www.r-sprint.org/.