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Primeur weekly 2013-12-16

The Cloud

How to offer wow in the Cloud? A unique book on the user experience provides help with service design ...

GreenButton launches WarpDrive for Cloud data transfers ...

NetApp introduces new all-flash array and performance-optimized enterprise storage systems ...

European Commission to issue report with Cloud standards ...

Alelo consolidates data centre and prepares for the Cloud with IBM PureSystems ...

EuroFlash

ISC'14 to issue Calls for tutorial proposals, research paper submissions and more ...

HPC Advisory Council and Swiss National Supercomputing Centre announce Switzerland Conference 2014 ...

IBM scientists demonstrate quantum phenomenon for the first time using a plastic film ...

DRIHM, a new EUDAT Associated Partner, collaborates to provide new services for citizen scientists ...

The University of Cambridge chooses Mellanox FDR InfiniBand to accelerate UK's fastest academic cluster and further space research ...

Minister for Economic Affairs and Competitiveness, Luis de Guindos and Catalonian Regional Minister of Economy and Knowledge, Andreu Mas-Colell, visit the Barcelona Supercomputing Center ...

Altair Engineering announces 7th European Altair Technology Conference - to be held in Munich, Germany from June 24-26, 2014 and invites customers and industry experts to submit presentation proposals ...

New supercomputer puts Bristol at the forefront of research ...

Super-fast and super-green: Cambridge unveils pioneering high-performance computer ...

USFlash

HPC Advisory Council announces HPCmusic subgroup ...

Qualcomm Technologies introduces Snapdragon 410 chipset with integrated 4G LTE World Mode for high-volume smartphones ...

Convey Computer's implementation of PacBioToCA algorithm speeds DNA sequence assembly, delivering up to fifteen times acceleration ...

Astrophysicists launch ambitious assessment of galaxy formation simulations ...

HP introduces innovations built for the data centre of the future ...

Third quarter HPC server revenues experience year-over-year decline as expected, following exceptional year-ago quarter, according to IDC ...

New York State awards University at Buffalo $1 million for supercomputer expansion ...

Iowa State-led team wins supercomputer time to study nuclear structures and reactions ...

Oracle SQL Developer 4.0 enhances support for Oracle Database 12c ...

Raritan adds new swappable sensor and mini plug-in sensor for monitoring data centre environments ...

Convey Computer's implementation of PacBioToCA algorithm speeds DNA sequence assembly, delivering up to fifteen times acceleration


11 Dec 2013 Richardson - Convey Computer Corporation has made the newest addition to Convey's expanding bioinformatics suite, PacBioToCA, an application that facilitates the assembly of genomes sequenced with Pacific Biosciences long-read technology. Optimized to take advantage of the highly parallel processing architecture of the Convey hybrid-core (HC) server, PacBioToCA delivers six to fifteen times acceleration.

Researchers running PacBioToCA on Convey HC systems for sequencing and assembly are seeing exceptional results. "The speed up is significant; but even more importantly, researchers are now able to test more parameters", commented Dr. George Vacek, Director of Convey Computer's Life Sciences business unit. "Achieving results in a matter of days instead of weeks allows them to refine their approach and get better answers."

The PacBio RS II DNA Sequencing System, from Pacific Biosciences, helps scientists solve genetically complex problems. Their single-molecule sequencing instruments can generate industry-leading sequence read lengths that dramatically improve genome and transcriptome assembly.

Researchers are attracted to the exceptionally long PacBio reads because they can deliver higher quality assemblies. Prior to the development of algorithms optimized for PacBio read data - such as PacBioToC, single-pass error rates had been perceived to limit their utility in de novo assembly.

Last year, Dr. Sergey Koren, Bioinformatics Scientist at the National Biodefense Analysis and Countermeasures Center, and his colleagues developed an assembly strategy that uses short sequences - either from PacBio circular consensus sequencing or short read technologies - typical of high-throughput sequencers to correct the errors in PacBio reads. This strategy was subsequently extended to use shorter single-molecule reads to correct the longest ones. These techniques deliver high-accuracy long reads, resulting in gold standard genome assemblies.

For larger genomes, the PacBioToCA algorithm can be time-consuming; therefore, Dr. Koren collaborated with Convey to optimize the PacBioToCA algorithm for Convey's highly parallel HC systems. The optimized version of PacBioToCA runs much faster on the Convey HC servers because the alignment algorithm it uses is significantly faster on a Convey HC-2ex server than the best implementation on a standard server.

"It has been shown that long PacBio reads processed with PacBioToCA lead to such high-quality assemblies, researchers are saved the significant subsequent cost of manual finishing", explained Kevin Corcoran, Senior Vice President of Market Development at Pacific Biosciences. "The combination of the

PacBioToCA algorithm and a Convey HC system allows our customers to dramatically speed up research for projects in areas such as functional genomics, comparative genomics, and beyond."

Convey's groundbreaking hybrid-core computing architecture tightly integrates advanced computer architecture and compiler technology with commercial, off-the-shelf hardware - namely Intel Xeon processors and Xilinx Field Programmable Gate Arrays (FPGAs). Particular algorithms are optimized and translated into code that's loaded onto the FPGAs at runtime to accelerate applications that use these algorithms. The systems help customers dramatically increase performance over industry standard servers while reducing energy costs associated with high-performance computing.

"Adding PacBioToCA to the Convey Bioinformatics Suite reflects our ongoing commitment to the bioinformatics and life sciences community", concluded Dr. Vacek. "We enjoy working with innovators to bring solutions to the industry that will help solve the challenges of the rapidly changing area of sequencing. We look forward to continuing to collaborate with Pacific Biosciences and others on optimization of bioinformatics work flows."

Convey's expanding bioinformatics suite is made up of a number of personalities including the Convey GraphConstructor for de novo short read assembly, Smith-Waterman for local sequence alignment, and Burrows-Wheeler Aligner for fast reference mapping.

Source: Convey Computer

Back to Table of contents

Primeur weekly 2013-12-16

The Cloud

How to offer wow in the Cloud? A unique book on the user experience provides help with service design ...

GreenButton launches WarpDrive for Cloud data transfers ...

NetApp introduces new all-flash array and performance-optimized enterprise storage systems ...

European Commission to issue report with Cloud standards ...

Alelo consolidates data centre and prepares for the Cloud with IBM PureSystems ...

EuroFlash

ISC'14 to issue Calls for tutorial proposals, research paper submissions and more ...

HPC Advisory Council and Swiss National Supercomputing Centre announce Switzerland Conference 2014 ...

IBM scientists demonstrate quantum phenomenon for the first time using a plastic film ...

DRIHM, a new EUDAT Associated Partner, collaborates to provide new services for citizen scientists ...

The University of Cambridge chooses Mellanox FDR InfiniBand to accelerate UK's fastest academic cluster and further space research ...

Minister for Economic Affairs and Competitiveness, Luis de Guindos and Catalonian Regional Minister of Economy and Knowledge, Andreu Mas-Colell, visit the Barcelona Supercomputing Center ...

Altair Engineering announces 7th European Altair Technology Conference - to be held in Munich, Germany from June 24-26, 2014 and invites customers and industry experts to submit presentation proposals ...

New supercomputer puts Bristol at the forefront of research ...

Super-fast and super-green: Cambridge unveils pioneering high-performance computer ...

USFlash

HPC Advisory Council announces HPCmusic subgroup ...

Qualcomm Technologies introduces Snapdragon 410 chipset with integrated 4G LTE World Mode for high-volume smartphones ...

Convey Computer's implementation of PacBioToCA algorithm speeds DNA sequence assembly, delivering up to fifteen times acceleration ...

Astrophysicists launch ambitious assessment of galaxy formation simulations ...

HP introduces innovations built for the data centre of the future ...

Third quarter HPC server revenues experience year-over-year decline as expected, following exceptional year-ago quarter, according to IDC ...

New York State awards University at Buffalo $1 million for supercomputer expansion ...

Iowa State-led team wins supercomputer time to study nuclear structures and reactions ...

Oracle SQL Developer 4.0 enhances support for Oracle Database 12c ...

Raritan adds new swappable sensor and mini plug-in sensor for monitoring data centre environments ...