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Primeur weekly 2011-07-18

The Cloud

Rutgers-led experts assemble globe-spanning supercomputer Cloud ...

IBM debuts Cloud-based analytics suite to help companies boost marketing results ...

HP accelerates customers' path to open, hybrid Cloud ...

IBM expands business in Japan with new Cloud data centres ...

VMware unveils VMware vSphere 5 and comprehensive Cloud infrastructure suite ...

Panaya reaches 2,000 ERP systems milestone ...

VMware introduces VMware vSphere Storage Appliance to further simplify IT for small and midsized businesses ...

ET Water celebrates smart irrigation month with the launch of the GNOME Smart Irrigation Calculator ...

From end-user to data centre: Cisco enhances Cloud computing performance, efficiency and security ...

Desktop Grids

Version 4.2.4 of OurGrid middleware released ...

XtremWeb-HEP 7.5.0 released ...

EuroFlash

Lomonosov supercomputer sets world record for performance on Graph500 benchmark ...

European Commission to organize Information Day on Cloud Computing, Internet of Services and Advanced Software Engineering ...

Bright Cluster Manager selected by Freie Universitaet Berlin to manage new Dell-based HPC system ...

Eurotech to receive 4 million euro order from Selex Elsag for Aurora HPC for cyber security applications ...

Medicsight and Ziooft partner in U.S. to offer computer-aided detection with supercomputing functional analytics ...

Imec achieves breakthroughs in enabling future DRAM and RRAM ...

USFlash

IBM Power Systems running Linux outperform competition on standard benchmarks ...

Drexel University chose advanced HPC and Bright Cluster Manager to help unravel the mysteries of the Universe and the world of molecular dynamics ...

Moving data at the speed of science: Berkeley Lab lays foundation for 100 Gbps prototype network ...

Scientists model physics of a key dark-energy probe ...

SDSC visualizations win 'OASCR' Awards at SciDAC 2011 ...

SDSC's Trestles provides rapid turnaround and enhanced performance for diverse researchers ...

Sandia's 'cooler' technology offers fundamental breakthrough in heat transfer ...

Changsha National Supercomputing Center inaugurated ...

Oracle introduces Oracle Exadata Storage Expansion Rack ...

University of Virginia's Olivier Pfister accomplishes breakthrough toward quantum computing ...

GNS Healthcare collaborates with NCI in new approach to lung cancer: supercomputer analysis to aid in matching targeted drugs to patients ...

Wolfram Research announces gridMathematica 8: Adding the power of CUDA over the Grid ...

UC Irvine study points to new approach to influenza's antiviral resistance ...

basysKom, Codero, Gluster and Nixu Open join The Linux Foundation ...

Stanford engineers build a nanoscale device for brain-inspired computing ...

NVIDIA names Stanford University a CUDA Center of Excellence ...

NIST prototype 'optics table on a chip' places microwave photon in 2 colours at once ...

UC Irvine study points to new approach to influenza's antiviral resistance

13 Jul 2011 San Diego - Researchers from the University of California, Irvine, with assistance from the San Diego Supercomputer Center at UC San Diego, have found a new approach to the creation of customized therapies for virulent flu strains that resist current antiviral drugs. The findings, published on-line inNature Communications, could aid development of new drugs that exploit so-called flu protein 'pockets'.

Using powerful computer simulations on SDSC's new Trestles system, launched earlier this year under a $2.8 million National Science Foundation (NSF) award, UCI's Rommie Amaro and Robin Bush together with SDSC's Ross Walker created a method to predict how pocket structures on the surface of influenza proteins promoting viral replication can be identified as these proteins evolve, allowing for possible pharmaceutical exploitation.

"Our results can influence the development of new drugs taking advantage of this unique feature", stated Rommie Amaro, an assistant professor of pharmaceutical sciences and computer science at UCI. Prior to joining UCI in 2009, Rommie Amaro was a postdoctoral fellow in chemistry at UC San Diego.

The search for effective flu drugs has always been hampered by the influenza virus itself, which mutates from strain to strain, making it difficult to target with a specific pharmaceutical approach. The most common clinical flu treatments are broad-based and only partially effective. They work by interrupting the action of an enzyme in the virus called neuraminidase, which plays a critical role in viral replication.

In 2006, scientists discovered that avian influenza neuraminidase (N1) exhibited a distinctive, pocket-shaped feature in the area pinpointed by clinically used drugs. They named it the 150-cavity.

Rommie Amaro and Robin Bush, associate professor of ecology and evolutionary biology, conducted research using resources at the San Diego Supercomputer Center, as well as the National Institute for Computational Sciences (NICS) to learn the conditions under which the pockets form. They created molecular simulations of flu proteins to predict how these dynamic structures move and change, as well as and where and when the 150-cavity pockets will appear on the protein surface.

This sequence analysis method could be utilized on evolving flu strains, providing vital information for drug design, Rommie Amaro said. "Having additional antivirals in our treatment arsenal would be advantageous and potentially critical if a highly virulent strain, for example, H5N1, evolved to undergo rapid transmission among humans or if the already highly transmissible H1N1 pandemic virus was to develop resistance to existing antiviral drugs", she added.

Ross Walker, an assistant research professor who runs the Walker Molecular Dynamics Lab at SDSC, developed a customized version of the AMBER software, a widely used package of molecular simulation codes, to run these specific simulations on Trestles under the NSF's TeraGrid Advanced User Support System. That included detailed performance tuning including hard-coding atom counts, atom types and parameters, and being able to use Trestles for uninterrupted two-week runs that together consumed more than one million SUs (single processor hours).

"We initially used the Athena supercomputer at NICS, which provided us with all the initial comparison data before Trestles came on-line earlier this year", stated Ross Walker, who is also an adjunct assistant professor in UC San Diego's Department of Chemistry and Biochemistry. "We had Trestles all ready to go as soon as the first H1N1 protein structure was available, and using the earlier work we did on Athena, we were able to put Trestles immediately to work to conduct simulations of the structure as part of this research."

Robert Swift and Lane Votapka of UCI, as well as Wilfred Li of UC San Diego, also contributed to the study, which received support from the National Institutes of Health and the NSF.
Source: University of California - San Diego

Back to Table of contents

Primeur weekly 2011-07-18

The Cloud

Rutgers-led experts assemble globe-spanning supercomputer Cloud ...

IBM debuts Cloud-based analytics suite to help companies boost marketing results ...

HP accelerates customers' path to open, hybrid Cloud ...

IBM expands business in Japan with new Cloud data centres ...

VMware unveils VMware vSphere 5 and comprehensive Cloud infrastructure suite ...

Panaya reaches 2,000 ERP systems milestone ...

VMware introduces VMware vSphere Storage Appliance to further simplify IT for small and midsized businesses ...

ET Water celebrates smart irrigation month with the launch of the GNOME Smart Irrigation Calculator ...

From end-user to data centre: Cisco enhances Cloud computing performance, efficiency and security ...

Desktop Grids

Version 4.2.4 of OurGrid middleware released ...

XtremWeb-HEP 7.5.0 released ...

EuroFlash

Lomonosov supercomputer sets world record for performance on Graph500 benchmark ...

European Commission to organize Information Day on Cloud Computing, Internet of Services and Advanced Software Engineering ...

Bright Cluster Manager selected by Freie Universitaet Berlin to manage new Dell-based HPC system ...

Eurotech to receive 4 million euro order from Selex Elsag for Aurora HPC for cyber security applications ...

Medicsight and Ziooft partner in U.S. to offer computer-aided detection with supercomputing functional analytics ...

Imec achieves breakthroughs in enabling future DRAM and RRAM ...

USFlash

IBM Power Systems running Linux outperform competition on standard benchmarks ...

Drexel University chose advanced HPC and Bright Cluster Manager to help unravel the mysteries of the Universe and the world of molecular dynamics ...

Moving data at the speed of science: Berkeley Lab lays foundation for 100 Gbps prototype network ...

Scientists model physics of a key dark-energy probe ...

SDSC visualizations win 'OASCR' Awards at SciDAC 2011 ...

SDSC's Trestles provides rapid turnaround and enhanced performance for diverse researchers ...

Sandia's 'cooler' technology offers fundamental breakthrough in heat transfer ...

Changsha National Supercomputing Center inaugurated ...

Oracle introduces Oracle Exadata Storage Expansion Rack ...

University of Virginia's Olivier Pfister accomplishes breakthrough toward quantum computing ...

GNS Healthcare collaborates with NCI in new approach to lung cancer: supercomputer analysis to aid in matching targeted drugs to patients ...

Wolfram Research announces gridMathematica 8: Adding the power of CUDA over the Grid ...

UC Irvine study points to new approach to influenza's antiviral resistance ...

basysKom, Codero, Gluster and Nixu Open join The Linux Foundation ...

Stanford engineers build a nanoscale device for brain-inspired computing ...

NVIDIA names Stanford University a CUDA Center of Excellence ...

NIST prototype 'optics table on a chip' places microwave photon in 2 colours at once ...