Computing boost for Rothamsted's science

2nd Aug 2012

Rothamsted Research has added TimeLogic's latest J1-series Field Programmable Gate Array (FPGA) hardware to their computational tools platform. This sophisticated technology will help Rothamsted scientists deliver the knowledge and innovation for environmentally sustainable solutions for food and energy agriculture, for example its 20:20 Wheat ® Programme.

TimeLogic's DeCypher systems greatly increase the speed of sequence comparison by combining custom field programmable gate array (FPGA) circuitry with optimized implementations of BLAST, Smith-Waterman, Hidden Markov Model and gene modeling algorithms. With the inclusion of this additional TimeLogic hardware, Rothamsted researchers now have a sizeable DeCypher system in-house, which significantly enhances their high-throughput genome annotation efforts.

According to Michael Murray, Manager of Sales and Marketing for TimeLogic products at Active Motif, "We have a long standing relationship with Rothamsted Research and their funding agency, the Biotechnology and Biological Sciences Research Council (BBSRC). This particular system represents an upgrade to an existing DeCypher system and we’re very proud of the fact that Rothamsted Research, like so many of our TimeLogic customers, continues to utilize our latest FPGA hardware revisions. Our recently announced J1-series FPGA platform will run Tera-BLAST, our accelerated BLAST implementation, over 960 times faster than running BLAST in software." Ted DeFrank, President of Active Motif added, "Recent advances in next-generation DNA sequencing technology have created great opportunities for our TimeLogic division and, as a result, Active Motif is investing heavily in this portion of our business. In addition to a major hardware revision, TimeLogic has several additional projects ongoing and we are excited about their continuation as we strive to further strengthen our position as the leader in the field of FPGA-accelerated Biocomputing solutions."

Dr. Jan Taubert, a Senior Bioinformatician in the Department of Computational and Systems Biology at Rothamsted - Harpenden added, "We are really excited about the latest products from TimeLogic and are going to use them to assist with our analysis of the recently sequenced wheat genome, process next generation DNA sequencing data from our studies of the microbial biodiversity of soils and to compare crop pathogen genomes". Prof. Christopher Rawlings, Head of the Department of Computational and Systems Biology at Rothamsted - Harpenden summarized, "The DeCypher system at Rothamsted is popular with our scientists because of its great performance and the simple web-based user interface. The increasing influx of next-generation DNA sequencing data and newly sequenced genomes from species relevant to our research in sustainable agriculture has led to our decision to expand in-house analysis capacity with the new DeCypher system. We are grateful to the support from the BBSRC that allowed us to make this new investment in our research e-infrastructure."

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