Novel HPC Technologies for Rapid Analysis in Bioinformatics

NSilico is an Irish based SME that develops software for the life sciences sector, providing bioinformatics and medical informatics systems to a range of clients. One of the major challenges that their users face is the exponential growth of high-throughput genomic sequence data and the associated computational demands to process such data in a fast and efficient manner. Genomic sequences contain gigabytes of nucleotide data that require detailed comparison with similar sequences in order to determine the nature of functional, structural and evolutionary relationships. In this regard NSilico has been working with computational experts from CINES (France) and ICHEC (Ireland) under the PRACE SHAPE programme to address a key problem that is the rapid alignment of short DNA sequences to reference genomes by deploying the Smith-Waterman algorithm on an emerging many-core technology, the Intel Xeon Phi co-processor. This white paper will discuss some of the parallelisation and optimisation strategies adopted to achieve performance improvements of the algorithm keeping in mind both existing and future versions of the hardware. The outcome has been an extremely successful collaboration between PRACE and NSilico, resulting in an implementation of the algorithm that can be readily deployed to realise significant performance gains from the next generation of many-core hardware