Welcome!

News Feed Item

New Convey GraphConstructor Leverages Hybrid-Core Architecture to Speed De Novo Genome Assembly

From Cows to Grapes, Efficient Use of Memory Fuels More Science

RICHARDSON, TX -- (Marketwire) -- 05/17/11 -- Convey Computer today introduced the Convey GraphConstructor™ (CGC), a new software and hardware solution that speeds up some of the world's most popular bioinformatics algorithms and helps scientists better manage and analyze escalating amounts of research data.

The Convey GraphConstructor accelerates construction and manipulation of de Bruijn graphs commonly used in short-read genome assembly applications such as Velvet (1) and Abyss. (2) The Convey GraphConstructor is the newest component in the company's bioinformatics suite.

"Convey's hybrid-core architecture provides powerful advantages to scientists dealing with large datasets across many disciplines. Nowhere is this more important than in bioinformatics -- where customers are achieving performance speed-ups from 2.2 to 8.4 times," (3) says Convey CEO and co-founder, Bruce Toal. "The Convey GraphConstructor helps researchers explore and manage the data deluge spilling from next-generation sequencing technologies faster and with significantly lower computing costs than in the past."

Key to improving performance and capability is Convey's novel hybrid-core computing architecture. Software-only applications are limited by the performance of commodity servers executing a stream of general-purpose instructions. Convey's architecture pairs classic Intel® x86 microprocessors with an FPGA-based coprocessor. This architecture allows key segments of an application -- DNA sequence alignment, for instance -- to run directly in hardware.

While raw processor performance increases are important, improved memory management is often just as important to increasing research throughput. Bioinformatics applications that depend upon random access patterns to large memory spaces, such as graph-based algorithms, experience severe memory performance limitations on cache-based x86 servers. Convey's highly parallel memory subsystem allows application-specific logic to concurrently access 8,192 individual words in memory, significantly increasing effective memory bandwidth over cache-based memory systems.

Many algorithms, such as Velvet and other de Bruijn graph based, short-read, de novo assemblers, greatly benefit from this type of memory architecture. Velvet author Dr. Daniel Zerbino says, "There are a number of engineering issues we didn't fully address in 2006 when we were developing Velvet and one of those issues was the hardware footprint. Memory size is the biggest difficulty. If your machine doesn't have enough memory, you must break down the problem and that can be quite a constraint for users. Convey's GraphConstructor offers a new approach to help researchers who want to test more parameters to achieve better assemblies or look at bigger jobs such as metagenomic or mammalian genome samples."

In fact, researchers at the U.S. Department of Energy/Joint Genome Institute (JGI) and the University of Mainz are currently using advanced computer architectures, such as hybrid-core computing and Convey's GraphConstructor, to tackle problems previously deemed impractical:

  • Cow Rumen Metagenome: As part of their work researching biofuels, JGI researchers want to discover how cows convert grass to gas so effectively. In January, JGI reported (Science, January 28, 2011) it had "sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen." The result so far is discovery of nearly 30,000 new enzymes for biofuel production improvements. Using a Convey hybrid-core computer and Convey's GraphConstructor helped JGI researchers speed up the discovery process by as much as 2.8 times and reduce the required memory footprint by up to 82 percent. (4)

  • Riesling Genome Assembly. In doing the first sequencing of the Riesling grape, University of Mainz researchers produced a dataset of 300 M reads, or 30 B nucleotides in size. Achieving an accurate assembly required using a fairly short kmer length, which drives up required memory and runtime. The existing computer system didn't have enough memory to complete the assembly with Velvet, but a Convey system running the Convey GraphConstructor was able to do so efficiently and without difficulty.

"Convey is solving a big problem here -- de novo assembly has been very difficult," says Dr. John Castle, head of Bioinformatics/Genomics at the Institute for Translational Oncology and Immunology (TrOn), University of Mainz. "At TrOn, we tried to assemble the Riesling genome with SOAPdenovo and with Velvet. Both failed because the computer ran out of memory. Other groups are trying to assemble grape genome as well but with mixed results, frequently due to hardware limitations. Convey, just by increasing the efficiency of Velvet, has made a significant accomplishment!"

Convey's use of reconfigurable technology and supercomputer-inspired memory management systems permit Convey hybrid-core systems to accelerate applications, drive next-generation solutions, and lower ownership costs. Convey's hybrid-core platforms include the HC-1 and the HC-1ex. For more information about Convey or the Convey GraphConstructor visit http://www.conveycomputer.com/

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. Convey brings decades of experience and intellectual assets to performance problem solving. Its executive and design teams all come from successful backgrounds of building computer companies, most notably Convex Computer Corporation and Hewlett-Packard. Convey Computer investors include Braemar Energy Ventures, CenterPoint Ventures, Intel Capital, InterWest Partners, Rho Ventures, and Xilinx. More information can be found at: www.conveycomputer.com.

(1) http://www.ebi.ac.uk/~zerbino/velvet/; Velvet is the most widely used program for de novo assembly of short-read sequences.
(2) http://www.ncbi.nlm.nih.gov/pubmed/19251739
(3) Performance varies considerably depending on problem size and specified kmer lengths.
(4) Poster, "Efficient Graph Based Assembly of Short-Read Sequences on a Hybrid-Core Architecture," DOE JGI User Meeting, Genomics of Energy and Environment, March 22-24, 2011, Walnut Creek, California.

Convey Computer, the Convey logo, Convey HC-1 and HC-1ex, and the Convey GraphConstructor are trademarks of Convey Computer Corporation in the U.S. and other countries. Intel® and Intel® Xeon® are registered trademarks of Intel Corporation in the U.S. and other countries. Xilinx is a registered trademark of Xilinx, Inc.

Add to Digg Bookmark with del.icio.us Add to Newsvine

More Stories By Marketwired .

Copyright © 2009 Marketwired. All rights reserved. All the news releases provided by Marketwired are copyrighted. Any forms of copying other than an individual user's personal reference without express written permission is prohibited. Further distribution of these materials is strictly forbidden, including but not limited to, posting, emailing, faxing, archiving in a public database, redistributing via a computer network or in a printed form.

Latest Stories
The cloud era has reached the stage where it is no longer a question of whether a company should migrate, but when. Enterprises have embraced the outsourcing of where their various applications are stored and who manages them, saving significant investment along the way. Plus, the cloud has become a defining competitive edge. Companies that fail to successfully adapt risk failure. The media, of course, continues to extol the virtues of the cloud, including how easy it is to get there. Migrating...
SYS-CON Events announced today that Super Micro Computer, Inc., a global leader in Embedded and IoT solutions, will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. Supermicro (NASDAQ: SMCI), the leading innovator in high-performance, high-efficiency server technology, is a premier provider of advanced server Building Block Solutions® for Data Center, Cloud Computing, Enterprise IT, Hadoop/Big Data, HPC and ...
18th Cloud Expo, taking place June 7-9, 2016, at the Javits Center in New York City, NY, will feature technical sessions from a rock star conference faculty and the leading industry players in the world. Cloud computing is now being embraced by a majority of enterprises of all sizes. Yesterday's debate about public vs. private has transformed into the reality of hybrid cloud: a recent survey shows that 74% of enterprises have a hybrid cloud strategy. Meanwhile, 94% of enterprises are using some...
Cloud computing delivers on-demand resources that provide businesses with flexibility and cost-savings. The challenge in moving workloads to the cloud has been the cost and complexity of ensuring the initial and ongoing security and regulatory (PCI, HIPAA, FFIEC) compliance across private and public clouds. Manual security compliance is slow, prone to human error, and represents over 50% of the cost of managing cloud applications. Determining how to automate cloud security compliance is critical...
How will your company move to the cloud while ensuring a solid security posture? Organizations from small to large are increasingly adopting cloud solutions to deliver essential business services at a much lower cost. According to cyber security experts, the frequency and severity of cyber-attacks are on the rise, causing alarm to businesses and customers across a variety of industries. To defend against exploits like these, a company must adopt a comprehensive security defense strategy that is ...
@DevOpsSummit taking place June 7-9, 2016 at Javits Center, New York City, and Nov 1-3, 2016, at the Santa Clara Convention Center in Santa Clara, CA, is co-located with the 18th International @CloudExpo and will feature technical sessions from a rock star conference faculty and the leading industry players in the world.
SYS-CON Events announced today that MangoApps will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. MangoApps provides modern company intranets and team collaboration software, allowing workers to stay connected and productive from anywhere in the world and from any device. For more information, please visit https://www.mangoapps.com/.
SYS-CON Events announced today that Catchpoint Systems, Inc., a provider of innovative web and infrastructure monitoring solutions, has been named “Silver Sponsor” of SYS-CON's DevOps Summit at 18th Cloud Expo New York, which will take place June 7-9, 2016, at the Javits Center in New York City, NY. Catchpoint is a leading Digital Performance Analytics company that provides unparalleled insight into customer-critical services to help consistently deliver an amazing customer experience. Designed...
SYS-CON Events announced today that EastBanc Technologies will exhibit at SYS-CON's 18th International Cloud Expo®, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. EastBanc Technologies has been working at the frontier of technology since 1999. Today, the firm provides full-lifecycle software development delivering flexible technology solutions that seamlessly integrate with existing systems – whether on premise or cloud. EastBanc Technologies partners with p...
The Internet of Things (IoT) is growing rapidly by extending current technologies, products and networks. By 2020, Cisco estimates there will be 50 billion connected devices. Gartner has forecast revenues of over $300 billion, just to IoT suppliers. Now is the time to figure out how you’ll make money – not just create innovative products. With hundreds of new products and companies jumping into the IoT fray every month, there’s no shortage of innovation. Despite this, McKinsey/VisionMobile data...
SYS-CON Events announced today that IBM Cloud Data Services has been named “Bronze Sponsor” of SYS-CON's 18th Cloud Expo, which will take place on June 7-9, 2016, at the Javits Center in New York City, NY. IBM Cloud Data Services offers a portfolio of integrated, best-of-breed cloud data services for developers focused on mobile computing and analytics use cases.
We’ve been doing it for years, decades for some. How many websites have you created accounts on? Your bank, your credit card companies, social media sites, hotels and travel sites, online shopping sites, and that’s just the start. We do it often without even thinking about it, quickly entering our personal information, our data, in a plethora of systems. Sometimes we’re not even aware of the information we are providing. It could be very personal information (think of the security questions you ...
In today's enterprise, digital transformation represents organizational change even more so than technology change, as customer preferences and behavior drive end-to-end transformation across lines of business as well as IT. To capitalize on the ubiquitous disruption driving this transformation, companies must be able to innovate at an increasingly rapid pace. Traditional approaches for driving innovation are now woefully inadequate for keeping up with the breadth of disruption and change facin...
As machines are increasingly connected to the internet, it’s becoming easier to discover the numerous ways Industrial IoT (IIoT) is helping to shape the business world. This is exactly why we have decided to take a closer look at this pervasive movement and to examine the desire to connect more things! Now if you need a refresher on IIoT and how it is changing the world, take a moment and listen to Greg Gorbach with ARC Advisory Group. Gorbach believes, "IIoT will significantly change the worl...
"What we see what happens when you have a completely networked society and the potential to now drive the value creation and the collaboration and the ecosystems that are possible when you start to be able to connect people and industries together in ways that have never been possible before," explained Esmeralda Swartz, VP of Marketing Enterprise & Cloud at Ericsson, in this SYS-CON.tv interview at @ThingsExpo, held November 3-5, 2015, at the Santa Clara Convention Center in Santa Clara, CA.