|By Marketwired .||
|May 17, 2011 10:00 AM EDT||
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.
(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.
The broad selection of hardware, the rapid evolution of operating systems and the time-to-market for mobile apps has been so rapid that new challenges for developers and engineers arise every day. Security, testing, hosting, and other metrics have to be considered through the process. In his session at Big Data Expo, Walter Maguire, Chief Field Technologist, HP Big Data Group, at Hewlett-Packard, will discuss the challenges faced by developers and a composite Big Data applications builder, foc...
Oct. 6, 2015 04:00 AM EDT Reads: 404
In his session at @ThingsExpo, Tony Shan, Chief Architect at CTS, will explore the synergy of Big Data and IoT. First he will take a closer look at the Internet of Things and Big Data individually, in terms of what, which, why, where, when, who, how and how much. Then he will explore the relationship between IoT and Big Data. Specifically, he will drill down to how the 4Vs aspects intersect with IoT: Volume, Variety, Velocity and Value. In turn, Tony will analyze how the key components of IoT ...
Oct. 6, 2015 04:00 AM EDT Reads: 243
Scott Guthrie's keynote presentation "Journey to the intelligent cloud" is a must view video. This is from AzureCon 2015, September 29, 2015 I have reproduced some screen shots in case you are unable to view this long video for one reason or another. One of the highlights is 3 datacenters coming on line in India.
Oct. 6, 2015 03:45 AM EDT Reads: 146
Recently announced Azure Data Lake addresses the big data 3V challenges; volume, velocity and variety. It is one more storage feature in addition to blobs and SQL Azure database. Azure Data Lake (should have been Azure Data Ocean IMHO) is really omnipotent. Just look at the key capabilities of Azure Data Lake:
Oct. 6, 2015 03:30 AM EDT Reads: 143
The cloud has reached mainstream IT. Those 18.7 million data centers out there (server closets to corporate data centers to colocation deployments) are moving to the cloud. In his session at 17th Cloud Expo, Achim Weiss, CEO & co-founder of ProfitBricks, will share how two companies – one in the U.S. and one in Germany – are achieving their goals with cloud infrastructure. More than a case study, he will share the details of how they prioritized their cloud computing infrastructure deployments ...
Oct. 6, 2015 03:00 AM EDT Reads: 668
Interested in leveraging automation technologies and a cloud architecture to make developers more productive? Learn how PaaS can benefit your organization to help you streamline your application development, allow you to use existing infrastructure and improve operational efficiencies. Begin charting your path to PaaS with OpenShift Enterprise.
Oct. 6, 2015 02:00 AM EDT Reads: 420
Decisions about budgets and resources are often made without IT even having a seat at the table. As technologist we understand the value of DevOps - but do your business counterparts? If they don't, your DevOps initiatives could lose funding before they start. In her session at DevOps Summit, Jeanne Morain, Strategist / Author at iSpeak Cloud, LLC, will provide insights on how to bridge the gap between business and technology leaders. Attendees will learn prescriptive guidance on balancing wor...
Oct. 6, 2015 02:00 AM EDT Reads: 564
The modern software development landscape consists of best practices and tools that allow teams to deliver software in a near-continuous manner. By adopting a culture of automation, measurement and sharing, the time to ship code has been greatly reduced, allowing for shorter release cycles and quicker feedback from customers and users. Still, with all of these tools and methods, how can teams stay on top of what is taking place across their infrastructure and codebase? Hopping between services a...
Oct. 6, 2015 02:00 AM EDT Reads: 346
SYS-CON Events announced today that Secure Infrastructure & Services will exhibit at SYS-CON's 17th International Cloud Expo®, which will take place on November 3–5, 2015, at the Santa Clara Convention Center in Santa Clara, CA. Secure Infrastructure & Services (SIAS) is a managed services provider of cloud computing solutions for the IBM Power Systems market. The company helps mid-market firms built on IBM hardware platforms to deploy new levels of reliable and cost-effective computing and hig...
Oct. 5, 2015 11:45 PM EDT Reads: 765
When it comes to IoT in the enterprise, namely the commercial building and hospitality markets, a benefit not getting the attention it deserves is energy efficiency, and IoT’s direct impact on a cleaner, greener environment when installed in smart buildings. Until now clean technology was offered piecemeal and led with point solutions that require significant systems integration to orchestrate and deploy. There didn't exist a 'top down' approach that can manage and monitor the way a Smart Buildi...
Oct. 5, 2015 11:45 PM EDT Reads: 199
SYS-CON Events announced today that IBM Cloud Data Services has been named “Bronze Sponsor” of SYS-CON's 17th Cloud Expo, which will take place on November 3–5, 2015, at the Santa Clara Convention Center in Santa Clara, CA. 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.
Oct. 5, 2015 11:00 PM EDT Reads: 608
Today, we are in the middle of a paradigm shift as we move from managing applications on VMs and containers to embracing everything that the cloud and XaaS (Everything as a Service) has to offer. In his session at 17th Cloud Expo, Kevin Hoffman, Advisory Solutions Architect at Pivotal Cloud Foundry, will provide an overview of 12-factor apps and migrating enterprise apps to the cloud. Kevin Hoffman is an Advisory Solutions Architect for Pivotal Cloud Foundry, and has spent the past 20 years b...
Oct. 5, 2015 10:45 PM EDT Reads: 689
While testing is often ignored when it comes to DevOps - it could be the most important aspect of achieving true DevOps success. Without rethinking automated testing from the ground-up, the entire DevOps productivity gain cannot be realized. Large tech companies build their own rapid test automation that runs in minutes across functional, performance, security and other tests. In his session at DevOps Summit, Kevin Surace, CEO of Appvance, will discuss how we learn from these real-world succe...
Oct. 5, 2015 10:00 PM EDT Reads: 419
DevOps has often been described in terms of CAMS: Culture, Automation, Measuring, Sharing. While we’ve seen a lot of focus on the “A” and even on the “M”, there are very few examples of why the “C" is equally important in the DevOps equation. In her session at @DevOps Summit, Lori MacVittie, of F5 Networks, will explore HTTP/1 and HTTP/2 along with Microservices to illustrate why a collaborative culture between Dev, Ops, and the Network is critical to ensuring success.
Oct. 5, 2015 09:45 PM EDT Reads: 691
SYS-CON Events announced today that Logz.io has been named a "Bronze Sponsor" of SYS-CON's @DevOpsSummit Silicon Valley, which will take place November 3-5, 2015, at the Santa Clara Convention Center in Santa Clara, CA. Logz.io provides open-source software ELK turned into a log analytics platform that is simple, infinitely- scalable, highly available, and secure.
Oct. 5, 2015 09:30 PM EDT Reads: 900