Navigation Links
DKFZ Installs Convey Hybrid-core Computers to Speed Next-Generation Sequencing
Date:8/15/2013

Richardson, TX (PRWEB) August 15, 2013

Convey Computer today announced that the German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) in Heidelberg, Germany, has installed two Convey hybrid-core (HC) computers. The Convey HC-2ex platforms are being used to accelerate the center’s next-generation sequencing (NGS) pipeline, saving them time and reducing energy consumption.

DKFZ tested their first Convey hybrid-core computer in the summer of 2012, using the server to accelerate a portion of their next-generation pipeline. Results were extremely positive; one of their initial jobs went from over 18 hours on an 8 core system to a mere 48 minutes on the Convey server.

Based on that success, DKFZ purchased two Convey HC-2ex servers a few months later. These hybrid-core systems were integrated into an existing 1,600 compute core cluster. The Convey systems are now routinely used at DKFZ in the production analysis for all BWA algorithms.

“We are extremely pleased with the Convey systems. Depending on the data, we are typically seeing between 10-20x acceleration, which is substantial,” explained Dr. Benedikt Brors, Group Leader Computational Oncology, Division Theoretical Bioinformatics at DKFZ. “And our entire workflow from one end to the other is reduced by a factor of two.”

Convey’s hybrid-core architecture pairs classic Intel® x86 microprocessors with a coprocessor comprised of field-programmable gate arrays (FPGAs). Particular algorithms—BWA-based alignment, for example—are optimized and translated into code that’s loadable onto the coprocessor at runtime. The result is order of magnitude performance increases with less power, space and cooling requirements.

The Heidelberg DKFZ facility currently processes 5 terabytes of data per day conducting NGS analysis. Prior to the Convey installation, processing massive amounts of data in a timely fashion was a challenge for DKFZ—both from a resource and time perspective.

One of the most time-consuming steps of analyzing a patient’s genome involves using the Burrows-Wheeler Aligner (BWA)–the preferred algorithm for fast, accurate alignment to a reference genome of the short reads typical of high-throughput sequencers (HTS). BWA was taking up to 80% of CPU time in the data center’s pipeline.

“Accelerating this portion of our pipeline allows us to get answers substantially faster,” noted Brors. “In addition, saving processing time reduces power consumption and cooling–which is a huge advantage in saving money and a step forward in our commitment to pursue green technologies.”

This DKFZ effort is part of the International Cancer Genome Consortium (ICGC) to study tumors from more than fifty types of cancers. Their goal is to develop better ways of diagnosing, treating and preventing many types of cancer. The scientists at DKFZ are currently participating in three different ICGC cancer research projects: pediatric brain tumors, malignant lymphoma, and prostate cancer. Their research focuses on mapping how cancer changes the genomes of cells and causes mutations within normal biological pathways.

About Convey Computer Corporation
Based in Richardson, Texas, Convey Computer breaks power, performance and programmability barriers with the world’s first hybrid-core computer—a system that marries the low cost and simple programming model of a commodity system with the performance of a customized hardware architecture. Using the Convey hybrid-core systems, customers worldwide in industries such as life sciences, research, advanced analytics, and government/defense are enjoying increased application performance and lower costs of ownership. http://www.conveycomputer.com.

All trademarks are the property of their respective owner. ™ and ® denote registered trademarks in the United States and other countries. Convey Computer and Convey HC-2 and HC-2ex are trademarks of Convey Computer Corporation in the U.S. and other countries.

Read the full story at http://www.prweb.com/releases/Convey/DKFZ/prweb11027803.htm.


'/>"/>
Source: PRWeb
Copyright©2012 Vocus, Inc.
All rights reserved

Related biology technology :

1. BGI Installs Roche GS FLX+ System to Enhance Long Read Sequencing Capabilities for Genome and Transcriptome Research
2. Renodis Installs Convenient Power Outlets to Allow Employee Charging of Electric Vehicles
3. The Genome Analysis Center Selects Convey to Support Next-Generation Sequencing
4. Convey Hybrid-core to Speed Genomic Research at Broad Institute
5. Nimbix and Convey Partner for “The Accelerated Genomics Cloud” (TAGC) Promotion
6. New research could mean faster computers and better mobile phones
7. Computers & Graphics incorporates Collage Authoring Environment
8. Tablet computers may interfere with settings on magnetically programmable shunt valves
9. Sapio Sciences Announces Exemplar LIMS for Tablet Computers
10. New 4-D transistor is preview of future computers
11. Quantum computers counting on carbon nanotubes
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/22/2016)...  According to Kalorama Information, the dominant trends ... include significant efforts in automation as well as ... affordable sequencers, say the healthcare market research firm, ... sample prep materials.  The healthcare market research company,s ... Next Generation Sequencing (NGS) , highlights major trends ...
(Date:6/22/2016)... DIEGO , June 22, 2016   ViaCyte, ... first pluripotent stem cell-derived islet replacement therapy for the ... presentations at ISSCR 2016 Annual Meeting.  ISSCR 2016, the ... to 25th at Moscone West in San Francisco.  ... of the presentations are as follows:Event: , Focus Session: ...
(Date:6/22/2016)... 22, 2016  Mesa Biotech Inc., a privately-held, ... platform designed specifically for point-of-care (POC) infectious disease ... advisory board (SAB). Approved by the executive leadership ... chartered to advise on the development and commercialization ... by Dr. Steve Young , this world-class ...
(Date:6/21/2016)... , June 22, 2016 Frontier Biotechnologies Inc. ... its novel patch product AB001 met primary endpoint at ... relief against placebo. Conducted at nine clinical centers in ... enrolled 146 patients with chronic low back pain. AB001 ... week-1 (p=0.024), (2) greater reduction than placebo in the ...
Breaking Biology Technology:
(Date:6/16/2016)... FRANCISCO , June 16, 2016 ... size is expected to reach USD 1.83 ... by Grand View Research, Inc. Technological proliferation and ... banking applications are expected to drive the market ... ) , The development of advanced ...
(Date:6/3/2016)... June 3, 2016 ... Nepal hat ein ... hochsicherer geprägter Kennzeichen, einschließlich Personalisierung, Registrierung und ... der Produktion und Implementierung von Identitätsmanagementlösungen. Zahlreiche ... im Januar teilgenommen, aber Decatur wurde als ...
(Date:5/24/2016)... care by providing unparalleled technology to leaders of the medical imaging industry.  As such, ... to the range of products distributed by Ampronix. Photo - http://photos.prnewswire.com/prnh/20160524/371420 ... ... ... With ...
Breaking Biology News(10 mins):