Optalysys Optical Co-processor Hits Milestone with GENESYS Project

By John Russell

February 12, 2018

Optalysys, a U.K company seeking to commercialize optical co-processor technology, today announced completion of its Genetic Search System (GENESYS) project conducted with the prestigious Earlham Institute (EI). Citing a dramatic power saving and performance speedup for computing a traditional genomics alignment problem, Optalysys says the work demonstrates the effectiveness and maturity of its optical processing technology, which the company promotes as a post-Moore’s Law alternative.

Broadly, Optalysys technology involves passing light through layers of tiny LCDs using a low power laser. Data is encoded by applying varying voltages to the LCDs which changes their optical density and modulates the resulting waveform. The net result is analogue encoding of numerical data onto the light. The emerging waveforms diffract from the LCD lattice and interact in ways that essentially perform Fourier transforms. By arranging LCDs it’s possible to perform a variety of functions.

Optalysys argues that because its optical processing approach is naturally parallel it eliminates the intense data management required to perform parallel processing on traditional (Von Neumann) processors and that it uses dramatically less energy and is faster (see link to short video on the technology below).

Optalysys System

The benchmark GENESYS project aligned metagenomics reads sequenced from the Human Microbiome Project Mock Community (a well characterized microbial community) against a database consisting of 20 bacterial genomes totaling 64 million base pairs. “The optical system exceeded the original targets delivering a 90 percent energy efficiency saving compared to the same test run on EI’s HPC cluster, with an accuracy comparable to the highly sensitive nucleotide form of BLAST, BLASTn (part of a family of Basic Local Alignment Search Tools used to compare query sequences with a library or database of sequences),” reported Optalysys.

Technology from the GENESYS project is launching in February 2018 as a cloud-based platform to a closed beta program of a select group of genomic institutes including EI, the University of Manchester, Oregon State University, and Zealquest Scientific Technology Co. in cooperation with the Shanghai Bioinformatics Center, Chinese Academy of Science.

Optalysys says the GENESYS technology holds promise for long-read sequence alignment, where speed improvements of several orders of magnitude over conventional software algorithms are possible – as well as in Deep Learning, specifically convolutional neural networks (CNNs).

“The collaboration with EI has been a great success,” said Nick New, founder and CEO of Optalysys in today’s release. “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.”

“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,“ said Daniel Mapleson, Analysis Pipelines Project Leader at EI who was the EI lead for the genomics tests during the project.

The GENESYS project was funded in part by U.K. Innovate, a government agency. Jon Mitchener, innovation lead for emerging technologies, Innovate UK, said, “GENESYS is a project that not only exemplifies the R&D done (combining novel optical HPC and deep learning AI techniques with a really important health-screening application), but also the way that support from Innovate UK can help accelerate the move from a prototype towards commercial product launch for a high-potential British SME like Optalysys.”

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