Optical hardware makes light work of DNA searches energy cost

The UK Government is providing more than £0.5m to fund a new optical processor system that will lower the energy consumption of carrying out DNA sequence searches and may be applicable to many other big data problems.

The UK’s Genome Analysis Centre (TGAC) based in Norwich, and a spin-out company from Cambridge University, Optalysys, are working together to develop and implement the new Genetic Search System (Genesys), which is based on an optical rather than electronic processor. Energy savings of more than 95 per cent per year are being claimed for the system.

Optalysys evolved from a University of Cambridge spin-out known as Cambridge Correlators Limited (CCL), specialising in photonics equipment such as lasers and sophisticated optics. Optalysys itself focuses on large-scale HPC applications and obtained £400,000 venture capital funding in 2014 and has just launched a Series A funding round to support product commercialisation activities up to the first product launches, expected in 2017.

The collaboration with the Genome Analysis Centre has been motivated by the fact that gene-sequencing technologies are outstripping the computational capacity to analyse their output. Public sequence databases are doubling in size every 18 months or so. This makes it very expensive to try to identify a newly sequenced gene by searching the databases for similar sequences that are already known. Such large databases require access to large HPC resources that consume energy for power and cooling.

It is hoped that the new Genetic Search System will be able to perform large-scale gene database searches powered by just a standard mains supply, thus reducing the capital and energy costs required to run searching software, such as BLAST. TGAC will be the first to apply the technology to the field of bioinformatics, where Optalysys's optical processing technology will be developed to perform BLAST-like searches against more than 64 million base-pairs of DNA within the Human Microbiome Mock Community database, which has been extensively studied at TGAC.

TGAC is strategically funded by a UK Government Research Council, BBSRC, and operates a national capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation. In addition, some £500,000 of funding for the project is coming from another UK Government agency, Innovate UK, whose mission is to provide new support for innovative small and medium-sized enterprises with high-growth potential.

Timothy Stitt, head of computing at TGAC, said that Optalysys’s optical computing hardware ‘has the potential to provide a step-change in the important areas of high-performance computing and energy efficiency, and I'm delighted that TGAC is leading the vanguard with this technology in the biosciences. Such a valuable collaboration between industry and academia is only possible through the support of funding bodies such as Innovate UK.’

However, the technology of Genesys is not limited to bio-informatics applications only. Once a successful prototype is realised, the technology can be transformed to be used for other projects relying on big data, such as real-time processing of satellite data and cancer diagnostics.

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