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.