|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.
You think you know what’s in your data. But do you? Most organizations are now aware of the business intelligence represented by their data. Data science stands to take this to a level you never thought of – literally. The techniques of data science, when used with the capabilities of Big Data technologies, can make connections you had not yet imagined, helping you discover new insights and ask new questions of your data. In his session at @ThingsExpo, Sarbjit Sarkaria, data science team lead ...
Apr. 29, 2016 09:15 PM EDT Reads: 251
The IoT has the potential to create a renaissance of manufacturing in the US and elsewhere. In his session at 18th Cloud Expo, Florent Solt, CTO and chief architect of Netvibes, will discuss how the expected exponential increase in the amount of data that will be processed, transported, stored, and accessed means there will be a huge demand for smart technologies to deliver it. Florent Solt is the CTO and chief architect of Netvibes. Prior to joining Netvibes in 2007, he co-founded Rift Technol...
Apr. 29, 2016 09:00 PM EDT Reads: 1,516
If there is anything we have learned by now, is that every business paves their own unique path for releasing software- every pipeline, implementation and practices are a bit different, and DevOps comes in all shapes and sizes. Software delivery practices are often comprised of set of several complementing (or even competing) methodologies – such as leveraging Agile, DevOps and even a mix of ITIL, to create the combination that’s most suitable for your organization and that maximize your busines...
Apr. 29, 2016 08:30 PM EDT Reads: 1,738
New Relic, Inc. has announced a set of new features across the New Relic Software Analytics Cloud that offer IT operations teams increased visibility, and the ability to diagnose and resolve performance problems quickly. The new features further IT operations teams’ ability to leverage data and analytics, as well as drive collaboration and a common, shared understanding between teams. Software teams are under pressure to resolve performance issues quickly and improve availability, as the comple...
Apr. 29, 2016 07:30 PM EDT Reads: 2,397
The proper isolation of resources is essential for multi-tenant environments. The traditional approach to isolate resources is, however, rather heavyweight. In his session at 18th Cloud Expo, Igor Drobiazko, co-founder of elastic.io, will draw upon their own experience with operating a Docker container-based infrastructure on a large scale and present a lightweight solution for resource isolation using microservices. He will also discuss the implementation of microservices in data and applicat...
Apr. 29, 2016 05:15 PM EDT Reads: 1,684
Join IBM June 8 at 18th Cloud Expo at the Javits Center in New York City, NY, and learn how to innovate like a startup and scale for the enterprise. You need to deliver quality applications faster and cheaper, attract and retain customers with an engaging experience across devices, and seamlessly integrate your enterprise systems. And you can't take 12 months to do it.
Apr. 29, 2016 04:30 PM EDT Reads: 1,765
See storage differently! Storage performance problems have only gotten worse and harder to solve as applications have become largely virtualized and moved to a cloud-based infrastructure. Storage performance in a virtualized environment is not just about IOPS, it is about how well that potential performance is guaranteed to individual VMs for these apps as the number of VMs keep going up real time. In his session at 18th Cloud Expo, Dhiraj Sehgal, in product and marketing at Tintri, will discu...
Apr. 29, 2016 04:30 PM EDT Reads: 616
Machine Learning helps make complex systems more efficient. By applying advanced Machine Learning techniques such as Cognitive Fingerprinting, wind project operators can utilize these tools to learn from collected data, detect regular patterns, and optimize their own operations. In his session at 18th Cloud Expo, Stuart Gillen, Director of Business Development at SparkCognition, will discuss how research has demonstrated the value of Machine Learning in delivering next generation analytics to im...
Apr. 29, 2016 03:45 PM EDT Reads: 1,596
This is not a small hotel event. It is also not a big vendor party where politicians and entertainers are more important than real content. This is Cloud Expo, the world's longest-running conference and exhibition focused on Cloud Computing and all that it entails. If you want serious presentations and valuable insight about Cloud Computing for three straight days, then register now for Cloud Expo.
Apr. 29, 2016 03:30 PM EDT Reads: 1,659
As you respond to increasing requests for new analytics, you need fast and flexible technology in your arsenal so that you can deploy the right workload to the right platform for the need at hand. Do you need self-service and fast time to value? Do you have data and application control and privacy needs, along with strict SLAs to meet? IBM dashDB™ is data warehouse technology powered by in-memory computing and in-database analytics that are designed for fast results, scalability and more.
Apr. 29, 2016 03:15 PM EDT Reads: 1,535
SYS-CON Events announced today that SoftLayer, an IBM Company, has been named “Gold Sponsor” of SYS-CON's 18th Cloud Expo, which will take place on June 7-9, 2016, at the Javits Center in New York, New York. SoftLayer, an IBM Company, provides cloud infrastructure as a service from a growing number of data centers and network points of presence around the world. SoftLayer’s customers range from Web startups to global enterprises.
Apr. 29, 2016 03:00 PM EDT Reads: 843
So, you bought into the current machine learning craze and went on to collect millions/billions of records from this promising new data source. Now, what do you do with them? Too often, the abundance of data quickly turns into an abundance of problems. How do you extract that "magic essence" from your data without falling into the common pitfalls? In her session at @ThingsExpo, Natalia Ponomareva, Software Engineer at Google, will provide tips on how to be successful in large scale machine lear...
Apr. 29, 2016 02:45 PM EDT Reads: 844
Up until last year, enterprises that were looking into cloud services usually undertook a long-term pilot with one of the large cloud providers, running test and dev workloads in the cloud. With cloud’s transition to mainstream adoption in 2015, and with enterprises migrating more and more workloads into the cloud and in between public and private environments, the single-provider approach must be revisited. In his session at 18th Cloud Expo, Yoav Mor, multi-cloud solution evangelist at Cloudy...
Apr. 29, 2016 02:30 PM EDT Reads: 1,402
IoT device adoption is growing at staggering rates, and with it comes opportunity for developers to meet consumer demand for an ever more connected world. Wireless communication is the key part of the encompassing components of any IoT device. Wireless connectivity enhances the device utility at the expense of ease of use and deployment challenges. Since connectivity is fundamental for IoT device development, engineers must understand how to overcome the hurdles inherent in incorporating multipl...
Apr. 29, 2016 02:30 PM EDT Reads: 1,406