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Primeur weekly 2012-10-08

The Cloud

ISC Cloud’12 shared new evolution images from HPC and big data in the Cloud ...

Bright Computing to present data aware Cloud bursting to the SLURM User Group ...

Oracle unveils expanded Oracle Cloud Services portfolio ...

Oracle extends Oracle Communications Billing and Revenue Management product family with innovative Oracle Communications Elastic Charging Engine ...

Oracle Enterprise Manager 12c introduces new tools and programmes for partners ...

Fujitsu Cloud solution bolsters Ritsumeikan Asia Pacific University's administrative information system ...

Lending Club selects Oracle ERP Cloud Service to help increase insight and efficiencies ...

Customers live on Oracle Fusion Human Capital Management ...

Oracle continues to extend industry's no. 1 business innovation platform for the enterprise and the Cloud ...

Kwality Dairy selects IBM Cloud to drive supply chain efficiencies ...

Oracle announces ISV integration with Oracle Sales and Marketing Cloud Service ...

Oracle unveils new partner Cloud programmes at Oracle OpenWorld 2012 ...

Fujitsu Cloud solution enhances Kansai University's educational research system platform ...

HP advances software-defined networks with integrated infrastructure, controller and application solutions ...

Oracle announces Oracle Solaris 11.1 at Oracle OpenWorld ...

VMware simplifies compliance for business-critical applications in the Cloud ...

Desktop Grids

OProject@Home has been launched ...

EuroFlash

Altair's latest Compute Manager offers built-in 3D and 2D visualization of high-performance computing simulations ...

Green Brain project to create an autonomous flying robot with a honey bee brain ...

Hi-fi single photons ...

USFlash

Indiana University develops tool to improve NASA polar ice mission ...

Launch of the USA's fastest Genomic Supercomputing Platform reduces cancer genome analysis from months to seconds - One patient every 47 seconds ...

South Australian Research Facility unleashes the Tizard supercomputer ...

Mellanox InfiniBand selected by Fujitsu to accelerate the Australian National University supercomputer ...

Oracle announces Oracle Exadata X3 Database In-Memory Machine ...

Virginia Tech to tackle the Big Data challenges of next-generation sequencing with HokieSpeed ...

Iowa State researchers developing Big Data toolbox to help genome researchers ...

IBM completes acquisition of Texas Memory Systems ...

Brown University awarded $1.5 million for new Big Data tools ...

Cognitech Inc. announces release of industry's fastest mobile and tower supercomputing Forensic Video Workstations ...

Dell Smart Grid Data Management Solution enables utility companies to improve efficiency ...

New Zealand Freight Service provider adopts IBM PureSystems for IT consolidation ...

IBM boosts security, Cloud and analytics capabilities with new Power systems, storage and mainframe technologies ...

Sandia builds Android-based network to study cyber disruptions ...

Sandia gains national recognition for sustainable energy management ...

NSF announces interagency progress on administration's Big Data initiative ...

National Science Foundation awards Rutgers $1.4 million to help create ways to analyze Big Data ...

Iowa State researchers developing Big Data toolbox to help genome researchers

3 Oct 2012 Ames - Today's life scientists are producing genomes galore. But there's a problem: The latest DNA sequencing instruments are burying researchers in trillions of bytes of data and overwhelming existing tools in biological computing. It doesn't help that there's a variety of sequencing instruments feeding a diverse set of applications.

Iowa State University's Srinivas Aluru is leading a research team that's developing a set of solutions using high performance computing. The researchers want to develop core techniques, parallel algorithms and software libraries to help researchers adapt parallel computing techniques to high-throughput DNA sequencing, the next generation of sequencing technologies.

Those technologies are now ubiquitous, "enabling single investigators with limited budgets to carry out what could only be accomplished by an international network of major sequencing centers just a decade ago", stated Srinivas Aluru, the Ross Martin Mehl and Marylyne Munas Mehl Professor of Computer Engineering at Iowa State.

"Seven years ago we were able to sequence DNA one fragment at a time", he stated. "Now researchers can read up to 6 billion DNA sequences in one experiment. How do we address these big data issues?"

A three-year, $2 million grant from the Big Data programme of the National Science Foundation and the National Institutes of Health will support the search for a solution by Srinivas Aluru and researchers from Iowa State, Stanford University, Virginia Tech and the University of Michigan. In addition to Srinivas Aluru, the project's leaders at Iowa State are Patrick Schnable, Iowa State's Baker Professor of Agronomy and director of the centres for Plant Genomics and Carbon Capturing Crops, and Jaroslaw Zola, a former research assistant professor in electrical and computer engineering who recently moved to Rutgers University.

The majority of the grant - $1.3 million - will support research at Iowa State. And Srinivas Aluru is quick to say that none of the grant will support hardware development.

Researchers will start by identifying a large set of building blocks frequently used in genomic studies. They'll develop the parallel algorithms and high performance implementations needed to do the necessary data analysis. And they'll wrap all of those technologies in software libraries researchers can access for help. On top of all that, they'll design a domain specific language that automatically generates computing codes for researchers.

Srinivas Aluru said that should be much more effective than asking high performance computing specialists to develop parallel approaches to each and every application.

"The goal is to empower the broader community to benefit from clever parallel algorithms, highly tuned implementations and specialized high performance computing hardware, without requiring expertise in any of these", stated a summary of the research project.

Srinivas Aluru said the resulting software libraries will be fully open-sourced. Researchers will be free to use the libraries while developing, editing and modifying them as needed.

"We're hoping this approach can be the most cost-effective and fastest way to gain adoption in the research community", Srinivas Aluru stated. "We want to get everybody up to speed using high performance computing."
Source: Iowa State University

Back to Table of contents

Primeur weekly 2012-10-08

The Cloud

ISC Cloud’12 shared new evolution images from HPC and big data in the Cloud ...

Bright Computing to present data aware Cloud bursting to the SLURM User Group ...

Oracle unveils expanded Oracle Cloud Services portfolio ...

Oracle extends Oracle Communications Billing and Revenue Management product family with innovative Oracle Communications Elastic Charging Engine ...

Oracle Enterprise Manager 12c introduces new tools and programmes for partners ...

Fujitsu Cloud solution bolsters Ritsumeikan Asia Pacific University's administrative information system ...

Lending Club selects Oracle ERP Cloud Service to help increase insight and efficiencies ...

Customers live on Oracle Fusion Human Capital Management ...

Oracle continues to extend industry's no. 1 business innovation platform for the enterprise and the Cloud ...

Kwality Dairy selects IBM Cloud to drive supply chain efficiencies ...

Oracle announces ISV integration with Oracle Sales and Marketing Cloud Service ...

Oracle unveils new partner Cloud programmes at Oracle OpenWorld 2012 ...

Fujitsu Cloud solution enhances Kansai University's educational research system platform ...

HP advances software-defined networks with integrated infrastructure, controller and application solutions ...

Oracle announces Oracle Solaris 11.1 at Oracle OpenWorld ...

VMware simplifies compliance for business-critical applications in the Cloud ...

Desktop Grids

OProject@Home has been launched ...

EuroFlash

Altair's latest Compute Manager offers built-in 3D and 2D visualization of high-performance computing simulations ...

Green Brain project to create an autonomous flying robot with a honey bee brain ...

Hi-fi single photons ...

USFlash

Indiana University develops tool to improve NASA polar ice mission ...

Launch of the USA's fastest Genomic Supercomputing Platform reduces cancer genome analysis from months to seconds - One patient every 47 seconds ...

South Australian Research Facility unleashes the Tizard supercomputer ...

Mellanox InfiniBand selected by Fujitsu to accelerate the Australian National University supercomputer ...

Oracle announces Oracle Exadata X3 Database In-Memory Machine ...

Virginia Tech to tackle the Big Data challenges of next-generation sequencing with HokieSpeed ...

Iowa State researchers developing Big Data toolbox to help genome researchers ...

IBM completes acquisition of Texas Memory Systems ...

Brown University awarded $1.5 million for new Big Data tools ...

Cognitech Inc. announces release of industry's fastest mobile and tower supercomputing Forensic Video Workstations ...

Dell Smart Grid Data Management Solution enables utility companies to improve efficiency ...

New Zealand Freight Service provider adopts IBM PureSystems for IT consolidation ...

IBM boosts security, Cloud and analytics capabilities with new Power systems, storage and mainframe technologies ...

Sandia builds Android-based network to study cyber disruptions ...

Sandia gains national recognition for sustainable energy management ...

NSF announces interagency progress on administration's Big Data initiative ...

National Science Foundation awards Rutgers $1.4 million to help create ways to analyze Big Data ...