Accelerated Blast for Bioinformatics: The University of Ghent Deploys TimeLogic's Latest FPGA Based DeCypher Solution for Genome Analysis
Ghent Belgium and Carlsbad, California (PRWEB) March 08, 2014 -- The Multidisciplinary Research Partnership on Bioinformatics “Nucleotides 2 Networks”, at Ghent University, has implemented TimeLogic’s latest J-Series Field Programmable Gate Array (FPGA) based DeCypher® system to assist researchers in their efforts to unravel the function of novel genes and proteins. TimeLogic’s DeCypher systems greatly increase the speed of sequence comparison by combining custom field programmable gate array (FPGA) based PCIe accelerator cards with high-performance servers to process optimized implementations of BLAST, Smith-Waterman, Hidden Markov Model and gene modeling algorithms.
“Our TimeLogic technology has been designed with large scale genome annotation projects in mind and these systems make a great addition to any compute facility. For example, this DeCypher® system will run Tera-BLAST, our accelerated BLAST implementation, many hundreds of times faster than the software-only version and as a result, can take quite a bit of pressure off your multi-core CPU cluster.” commented Michael Murray, Manager of Sales & Marketing activities for TimeLogic products at Active Motif. Furthermore, he added, “this purchase represents the expansion of an existing DeCypher system and we’re very proud of the fact that Ghent University, like so many of our TimeLogic customers, continues to update their DeCypher platform with the inclusion of our latest FPGA hardware.”
Prof. Van de Peer from Ghent University added, “Recent (r)evolutions in sequencing technologies cause an exponential increase in the number of nucleotide and protein sequences deposited in sequence databases. This is posing serious challenges for even the most basic bioinformatics analyses such as simple sequence similarity searches through sequence alignment. To perform these types of analyses we usually rely on large computer clusters. However, such large computer clusters are not always optimally suited for some of the analyses we need. In particular for sequence comparisons, the Decypher solution offered by TimeLogic opens up new possibilities and drastically increases efficiency.”
Prof. Van de Peer continues, “The performance, administrative convenience, and value (cost per computing unit) of this system makes it an ideal choice for the computational biology research performed at Ghent University, allowing all UGhent MRP partners to conduct analyses that would otherwise take too long or even be impossible”.
About the Multidisciplinary Research Partnership on Bioinformatics “Nucleotides 2 Networks” (N2N), at Ghent University.
The Multidisciplinary Research Partnership N2N (from Nucleotides to Networks) can be considered a Center of Excellence in Bioinformatics and Systems Biology, established at Ghent University. Recent evolutions in data-producing technologies have dramatically changed the way we tackle problems in molecular biology and has created a huge need for highly trained scientists, with very diverse backgrounds, to collect, store, and analyze these data using advanced ICT infrastructures and bioinformatics tools. For bioinformatics and systems biology to be truly successful, computer scientists, physicists, mathematicians, statisticians, engineers, and molecular biologists need to join forces. These different backgrounds will enable the scientists to work closely together to (1) deal with the ever-growing amounts of biological data, (2) serve an ever-demanding community of molecular experimental biologists, bioengineers, and medical doctors, and (3) to address the bigger questions in biology through integrated systems biology approaches.
The MRP N2N consists of researchers from 10 different Departments and 6 different Faculties, totaling to about 100 researchers addressing emerging problems in molecular biology.
For more information on this UGent Partnership please visit http://www.nucleotides2networks.be.
About Ghent University
With more than 40,000 students and over 8000 staff members, Ghent University is one of the leading institutions of higher education and research in the Low Countries. Ghent University is an open, societal committed and pluralistic university with a broad international perspective.
With a view to cooperation in research and scientific service, numerous research groups, centers and institutes have been founded over the years. Several of them are renowned worldwide, in various scientific disciplines such as biotechnology, bioinformatics, aquaculture, microelectronics, history, and so on …
Located in Flanders, the Dutch-speaking part of Belgium and the cultural and economic heart of Europe, Ghent University is an active partner in national and international educational, scientific and industrial cooperation.
About Active Motif
TimeLogic, a division of Active Motif, Inc, is the world leader in accelerating genome annotation tools using Field Programmable Gate Array (FPGA) technology. The blend of powerful FPGA hardware with optimized bioinformatics applications produces a perfect combination of performance, accuracy and value. These DeCypherTM systems are also simple to use & 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 La Hulpe, 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(at)activemotif(dot)com.
Michael Murray, http://www.activemotif.com/catalog/75/timelogic-biocomputing-solutions, +1 (760) 431-1263 Ext: 347, [email protected]
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