News › Computing boost for Rothamsted's science

The Centenary Building in Harpenden

30 July 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."

Contacts

› Chris Rawlings and Jan Taubert

Notes to Editors

About TimeLogic

TimeLogic, a division of Active Motif, Inc, is the world leader in hardware accelerated bioinformatics search tools which accelerate genome annotation by combining optimized bioinformatics applications with powerful FPGA-based PCIe accelerator cards. This blend of specialized hardware and optimized software provides a perfect combination of performance, accuracy and value. Furthermore, these systems are simple to maintain and scale easily. Utilizing a TimeLogic system reduces pressure on over-used CPU-clusters by off-loading BLAST, Smith-Waterman (SW) and Hidden Markov Model (HMM) tasks to a highly time and energy efficient solution. From the earliest genome sequencing projects in the 1990’s to the largest metagenomics projects undertaken to date, TimeLogic has provided the enabling technology to make this research possible. Active Motif/TimeLogic operates globally through its corporate headquarters in Carlsbad, California, European headquarters in Rixensart, Belgium and Japanese headquarters in Tokyo, Japan. Active Motif/TimeLogic applies a multi-disciplinary approach to create new and modify existing technologies to meet the current and future needs of life science researchers.

Find out more by visiting us at http://www.timelogic.com or contact Michael Murray at tlsales@activemotif.com

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Rothamsted Research Press Office

For further information, please contact Darren Hughes, Head of Communications, on +44 (0) 1582 763 133 ext 2673, email darren.hughes@rothamsted.ac.uk

Rothamsted is the longest running agricultural research station in the world, providing cutting-edge science and innovation for nearly 170 years. Our mission is to deliver the knowledge and new practices to increase crop productivity and quality and to develop environmentally sustainable solutions for food and energy production. Our strength lies in our integrated, multidisciplinary approach to research in plant and soil science.

Rothamsted Research receives strategic funding from the Biotechnology and Biological Sciences Research Council (BBSRC) . It is the longest running agricultural research station in the world, developing environmentally sustainable solutions for food and energy production through science and innovation for nearly 170 years.

About BBSRC

BBSRC is the UK funding agency for research in the life sciences and the largest single public funder of agriculture and food-related research.

Sponsored by Government, BBSRC's budget for 2011-12 is around £445M which it is investing in a wide range of research that makes a significant contribution to the quality of life in the UK and beyond and supports a number of important industrial stakeholders, including the agriculture, food, chemical, healthcare and pharmaceutical sectors.

BBSRC provides institute strategic research grants to the following:

The Babraham Institute, Institute for Animal Health, Institute for Biological, Environmental and Rural Sciences (Aberystwyth University), Institute of Food Research, John Innes Centre, The Genome Analysis Centre, The Roslin Institute (University of Edinburgh) and Rothamsted Research.

The Institutes conduct long-term, mission-oriented research using specialist facilities. They have strong interactions with industry, Government departments and other end-users of their research.

For more information see: www.bbsrc.ac.uk