Is optical computing set to reboot genomics research?

Image: Wikimedia / Clique
Ingrid Fadelli

Meet the British startup developing  genomics research technology that could complete calculations quicker using less energy

Optalysis, a UK-based tech startup, is currently developing optical computing tools that is possibly set to make serious inroads in to the limitations in speed and the energy appetite of current computers.

The company’s technology could have interesting implications for genomics research, helping scientists to search through DNA faster and consuming considerably less power.

An optical computer, also referred to as ‘photonic computer’, is a computer that performs digital computations using photons in visible light or Infrared (IR) beams instead of electricity.

In 1965, American engineer and Intel’s co-founder Gordon Moore observed that the number of transistors per square inch of integrated circuits had doubled every year since their invention and predicted that this trend will continue in years to come.

This prediction became known as Moore’s Law and he later revisited it in 1975, extending the time to two years.

So far, this has proven to be correct, yet technology experts predict that, by 2021, it may no longer be economically possible to shrink transistors further, slowing down Moore’s law or ending it entirely.

This would pose a limit in what traditional computer processors are capable of doing, calling for new computing techniques to enhance performance further.

Optical computing methods are one of the ways in which engineers could achieve faster speeds for computational calculations, while also saving considerable amounts of energy.

However, researchers in the field have been facing numerous challenges and there have been relatively few developments in related technologies.

Researchers still debate whether this type of machine will ever be able to compete with traditional computers in terms of power consumption, cost, and speed.

Optalysys has set out to explore the possibilities of optical computing and has recently developed processors that could be applied to complex genomics research.

A faster way of searching through DNA sequences

Optalysys is a pioneer in the development of optical processors that has been trying to address the possible collapse of Moore’s law by creating solutions that could increase processing speeds and reduce energy consumption.

Their processor uses laser beams to perform a type of mathematical functions known as Fourier transforms; executing calculations that a traditional computer would do in several stages, but in a single step.

The startup says that its first product can perform Fourier transform functions 10 times faster than an Nvidia P6000 graphics card, which is generally used for high-performance computation, but using only 25% of its power.

The optical hardware necessary to complete these calculations is placed on a Peripheral Component Interconnect (PCI to you and me) card so it can fit into traditional desktops and servers.

This processor could be particularly useful in identifying similarities in complex data, which is a vital aspect of genomics research.

Optalysys have also developed a software tool that uses optical computing hardware to quickly identify short portions of DNA within infinite genome-sequences, which could be of immeasurable value for genetics research.

The company has recently teamed up with several genomics institutes, including the Earlham Institute, a life science research organization based in Norwich (UK); the University of Manchester (UK); The University of York (UK) Oregon State University (US); and other institutions on a quest to use optical computing for large-scale DNA sequence alignment.

The institutions have started beta-testing Optalysys’ hardware to search for similarities in DNA sequences and today the company announced the completion of the Genetic Search System (GENESYS) project, which involved an initial testing of the system.

Cheap at twice the price

The project, which received £0.5m in funding, saw the Earlham institute testing the new technology for large-scale DNA sequence alignment.

The institute used the tool to align metagenomic reads sequenced from the Human Microbiome Project Mock Community, against a database of 20 bacterial genomes that had a total of 62 million base pairs.

“The collaboration with EI has been a great success,” said Dr. Nick New, founder and CEO of Optalysys. “We have demonstrated the technology at several international conferences including Advances in Genome Biology and Technology, Plant and Animal Genome Conference and Genome 10K/Genome Science, to an overwhelmingly enthusiastic response. We are looking forward to continuing our strong relationship with EI through the beta program and beyond.”

The results of the GENESYS project were impressive, exceeding original targets. Optalysys’ platform reached 90% of energy efficiency saving, with an accuracy similar to that of advanced tools that are currently in use.

Dr. Daniel Mapleson, the EI lead for the genomics tests during the project, said:  “Genomic institutes are being faced with analyzing more and more data, and it is really exciting that new technologies like the Optalysys optical processing platform can support bioinformaticians processing data accurately, at a low cost and at high speeds.”

Research using optical computing tools

The optical computing platform developed by Optalysys has already achieved surprising results for genomics research and it could soon be applied to other fields as well.

The GENESYS project revealed that the system holds promise for long-read sequence alignment and for applications in the use of deep learning algorithms.

Now, the company is exploring ways in which its hardware could speed up AI image recognition capabilities.

Optalysys is planning to release a commercial version of its hardware and DNA software in the summer, the cost of which is still unknown.

While the startup’s optical computing platform might struggle to reach widespread adoption, it could be incredibly valuable within research settings, helping scientists to complete time-consuming tasks at much faster speeds, potentially saving lives as well as energy.

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