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Primeur monthly 2011-05-

Industry

Cisco announces intent to acquire newScale ...

GigaSpaces announces new product for enterprise PaaS & ISV SaaS enablement ...

HP accelerates channel partner Cloud opportunities ...

Coca-Cola FEMSA signs $100 million technology services agreement with HP to support growth ...

HP defines go-to-market strategy for Connected World at Americas Partners Conference ...

HP opens new research facility to advance sustainable data centre technologies ...

U.S. Special Operations Command selects HP for worldwide data centre services ...

IBM launches Power Development Lab in Taiwan ...

IBM Watson goes to school to engage next generation of innovators ...

Cameroon Ministry of Finance selects IBM mainframe system ...

Microsoft survey reveals 39 percent of SMEs to pay for Cloud services within three years ...

Platform Computing Announces Support for MapReduce ...

Red Hat reports fourth quarter and fiscal year 2011 results ...

Antarctic icebergs play a key role in the carbon cycle ...

SDSC's CIPRES Gateway provides window to the past - and fast ...

SGI Channel Network Programme receives CRN's Five-Star Partner rating designation for second year in a row ...

Researchers in Taiwan to use volunteer computing to visualise earthquakes ...

University of Westminster launches new DIY supercomputer saving hundreds of thousands of pounds ...

Ian Foster to receive IEEE Computer Society's Tsutomu Kanai Award ...

Digital infrastructure, Cloud computing transforming fragmented manufacturing industry value chain, according to Microsoft study ...

Presentations from the 27th ORAP Forum now available ...

University of Texas at Austin dedicates Lonestar 4 supercomputer for open science community ...

UK Atomic Weapons Establishment accelerates engineering efforts with SGI Altix UV ...

SGI offers free technical computing Cloud services in Japan to help customers in affected areas ...

Hewlett-Packard/American Chemical Society Award given for computational chemistry ...

Yale purchases world-class supercomputer ...

Calculations with 14 quantum bits ...

Cycle Computing creates a 10,000 core cluster in the Cloud ...

Breakthrough study confirms cause of short gamma-ray bursts ...

OSU chemist developing solution to nerve agent exposure ...

University of Minnesota Supercomputing Institute expands resources with addition of new supercomputer ...

Cray CX1000 supercomputer to feature the new Intel Xeon processor E7 family ...

Xerox chooses bullion to virtualize its critical business applications ...

IBM's MRSA infection-fighting nanotechnology caps century of health care innovation ...

Version 3.1 of BOINC LCS now available ...

TThrottle version 3.41 has been released ...

Dell invests $1 billion in technology solutions and services to help customers drive business results today and in the future ...

"Lonestar 4" supercomputer deployed for science community ...

SDSC to open large-scale data systems research centre ...

PRACE Research Infrastructure grants 400 million compute hours on Tier-0 systems to seventeen European research projects ...

Industry leaders worldwide embrace IBM Clouds to transform business processes ...

IBM joins forces with over 45 organisations to launch Cloud Standards Customer Council for Open Cloud Computing ...

Bird Hosting expands Cloud service offerings powered by CA 3Tera AppLogic software and signs multi-year license agreement ...

Elsevier special issue on "Models and Algorithms for High-Performance Distributed Data Mining" to issue Call for Papers ...

IBM sets performance records with new eX5 servers ...

CA Technologies acquires IT consulting firm, Base Technologies ...

EMC helps Blue Diamond Solutions deliver Cloud based back-up ...

SAS to offer high-performance analytics on EMC Greenplum database appliance ...

IBM unveils next generation SmartCloud platform for business ...

SAS High-Performance Analytics on Teradata appliance extends analytic innovation to customers ...

Microsoft and Toyota announce strategic partnership on next-generation telematics ...

IBM unveils smart Cloud services and technologies for the enterprise ...

Latest CA Workload Automation release enables dynamic service and application automation across physical, virtual and Cloud infrastructures ...

Dell ups the performance bar on Powerhouse servers for mission critical workloads and applications ...

Electric Yellowstone - Conductivity image hints volcano plume is bigger than thought ...

Savtira Corporation selects Emerson Network Power for data centre infrastructure solution ...

New IBM software helps clients accelerate adoption and realize the benefits of Cloud computing ...

Intel Xeon processor E7 family delivers record-breaking performance, new security, reliability and energy efficiency features ...

PSSC Labs to showcase bionformatics supercomputer and other life science compute & storage solutions at BIO IT World ...

SAS OnDemand for Academics to be available at no cost for research ...

Altair Engineering announces the release of MindManager through the HyperWorks Partner Alliance ...

Joint European DCI Summer School to issue Call for Participation ...

EDGI demonstrates how to submit 10,000 jobs to a Volunteer Desktop Grid from within the European Grid Infrastructure ...

Blood vessel simulation probes secrets of brain ...

International research on controlled nuclear fusion: Bull is selected to provide the supercomputer to be installed in Rokkasho, Japan ...

EGI Technical Forum 2011 to be held in September in Lyon ...

Bull TrustWay Hardware Security Module now integrates with Oracle Advanced Security for Oracle Database 11g ...

4th IEEE International Conference on Utility and Cloud Computing to issue Call for Papers ...

EMC Isilon delivers breakthrough performance for big data ...

IBM teams with Akamai to accelerate applications across the web, and from the Cloud to the enterprise ...

IBM offers new opportunities to jump start Cloud computing for business partners and start-ups ...

IBM to deliver new optimized POWER7 products, inspired by Watson technology ...

Tate & Lyle Sugar's refining operations step into the Cloud with Virtustream and IBM ...

IBM and Sybase harness POWER7 for new mCommerce Appliance ...

Networking

HP helps VIVACOM integrate fixed and mobile networks for better services ...

Europe

e-IRG welcomes public comment on the e-IRG White Paper 2011 ...

SDSC's CIPRES Gateway provides window to the past - and fast

28 Mar 2011 San Diego - A novel supercomputing resource created by researchers at the San Diego Supercomputer Center at the University of California, San Diego, is allowing scientists to study evolutionary relationships among large populations of living things in significantly shorter times - and without having to understand how to operate large, complex computer systems. The new resource, called the CIPRES - Cyberinfrastructure for Phylogenetic RESearch - Gateway, is an Internet portal that allows scientists anywhere in the world to upload their data via a standard Web browser and perform phylogenetic analyses. The most time-consuming analyses use supercomputers, such as SDSC's new Trestles system, that are part of the National Science Foundation's TeraGrid, the world's most powerful collection of high-performance computing resources dedicated to academic research.

"In addition to answering the age-old questions of how all living things are related to each other, understanding evolutionary relationships has some very important practical benefits", stated Mark Miller, principal investigator in SDSC's Research, Education and Development group, and leader of the CIPRES Gateway project. "For example, knowing the evolutionary relationships among a group of viruses or bacteria can help doctors understand where an infection came from, effectively treat patients who are infected, and work to contain the spread of disease during an outbreak."

Moreover, understanding how individual species adapt for survival in a specific geographic location can help scientists manage a species for long-term survival in that location, or engineer crops for higher productivity in a particular location.

Evolutionary relationships are uncovered by comparing DNA sequences from individuals under study. Just as a single DNA sequence can be used to identify a criminal with a very high degree of accuracy, a group of DNA sequences can be used to determine just how closely related any group of living things are with great precision.

"DNA sequences from individuals can be prepared so quickly and cheaply now, we can understand evolutionary relationships more accurately than ever before", according to Mark Miller. "The problem is, the number of computations required grows quickly as the amount of data grows. There are only three possible relationships between any four individuals, but there are more than two million different relationships between 10 individuals. A computer that could analyze a million trees per second would require about 20 billion years to test all the possible relationships for just 22 individuals."

Solving this problem is where the CIPRES Gateway and TeraGrid supercomputers come in. The power of supercomputers comes from parallel computing, in which large analyses are broken into smaller pieces that are run simultaneously on many processor cores. Under the TeraGrid's Advanced User Support programme, Wayne Pfeiffer, a distinguished scientist at SDSC, helped improve the parallel performance of RAxML and MrBayes, two widely used phylogenetics codes.

"Most RAxML analyses submitted to the CIPRES Gateway now run on 60 cores of Trestles", stated Wayne Pfeiffer. "With a typical speedup over a single core of about 30, this means that analyses that would require a month on a laptop can be completed in a day via the gateway."

"This is an excellent example of how science is being transformed through new ways of leveraging the capabilities of today's supercomputers", stated Richard Moore, SDSC's deputy director. "Significantly reducing the time it takes researchers to run such complex analyses, while freeing them from having to fully understand all the intricacies of today's supercomputers, means greater scientific productivity. This is what makes the CIPRES Gateway such a valuable phylogenetic resource."

Although SDSC's CIPRES Gateway has been in operation for a little more than a year, it has already provided immediate benefits to the scientific community, both in time savings and in new discoveries. To date, more than 2,000 scientists have run more than 35,000 analyses for approximately 100 completed studies. These studies span a broad spectrum of biological and medical research.

One study, recently published in the journalParisitology, focused on research that showed humans are much more likely to infect apes with malaria, than the reverse.

"Without the CIPRES Gateway, this work, and the other projects I am working on, would not go as quickly or as smoothly", stated James B. Munro, a researcher from the University of Maryland School of Medicine, who was part of the research team that reported the new insights into the complex relationship between the malarial parasites and their mammalian hosts.

CIPRES was a five-year project among 16 institutions, and funded by the NSF from 2003-2008. Its goal was to enable large-scale phylogenetic reconstructions on a scale that supports analyses of huge data sets containing hundreds of thousands of biomolecular sequences and to create an infrastructure that continues to support phylogenetic investigations. Ongoing projects include the CIPRES Gateway, as well as TreeBaseII, a repository of user-submitted phylogenetic trees and the data used to generate them, and Crimson, a database that facilitates the extraction of sub-trees from very large phylogenetic trees.
Source: University of California - San Diego

Back to Table of contents

Primeur monthly 2011-05-

Industry

Cisco announces intent to acquire newScale ...

GigaSpaces announces new product for enterprise PaaS & ISV SaaS enablement ...

HP accelerates channel partner Cloud opportunities ...

Coca-Cola FEMSA signs $100 million technology services agreement with HP to support growth ...

HP defines go-to-market strategy for Connected World at Americas Partners Conference ...

HP opens new research facility to advance sustainable data centre technologies ...

U.S. Special Operations Command selects HP for worldwide data centre services ...

IBM launches Power Development Lab in Taiwan ...

IBM Watson goes to school to engage next generation of innovators ...

Cameroon Ministry of Finance selects IBM mainframe system ...

Microsoft survey reveals 39 percent of SMEs to pay for Cloud services within three years ...

Platform Computing Announces Support for MapReduce ...

Red Hat reports fourth quarter and fiscal year 2011 results ...

Antarctic icebergs play a key role in the carbon cycle ...

SDSC's CIPRES Gateway provides window to the past - and fast ...

SGI Channel Network Programme receives CRN's Five-Star Partner rating designation for second year in a row ...

Researchers in Taiwan to use volunteer computing to visualise earthquakes ...

University of Westminster launches new DIY supercomputer saving hundreds of thousands of pounds ...

Ian Foster to receive IEEE Computer Society's Tsutomu Kanai Award ...

Digital infrastructure, Cloud computing transforming fragmented manufacturing industry value chain, according to Microsoft study ...

Presentations from the 27th ORAP Forum now available ...

University of Texas at Austin dedicates Lonestar 4 supercomputer for open science community ...

UK Atomic Weapons Establishment accelerates engineering efforts with SGI Altix UV ...

SGI offers free technical computing Cloud services in Japan to help customers in affected areas ...

Hewlett-Packard/American Chemical Society Award given for computational chemistry ...

Yale purchases world-class supercomputer ...

Calculations with 14 quantum bits ...

Cycle Computing creates a 10,000 core cluster in the Cloud ...

Breakthrough study confirms cause of short gamma-ray bursts ...

OSU chemist developing solution to nerve agent exposure ...

University of Minnesota Supercomputing Institute expands resources with addition of new supercomputer ...

Cray CX1000 supercomputer to feature the new Intel Xeon processor E7 family ...

Xerox chooses bullion to virtualize its critical business applications ...

IBM's MRSA infection-fighting nanotechnology caps century of health care innovation ...

Version 3.1 of BOINC LCS now available ...

TThrottle version 3.41 has been released ...

Dell invests $1 billion in technology solutions and services to help customers drive business results today and in the future ...

"Lonestar 4" supercomputer deployed for science community ...

SDSC to open large-scale data systems research centre ...

PRACE Research Infrastructure grants 400 million compute hours on Tier-0 systems to seventeen European research projects ...

Industry leaders worldwide embrace IBM Clouds to transform business processes ...

IBM joins forces with over 45 organisations to launch Cloud Standards Customer Council for Open Cloud Computing ...

Bird Hosting expands Cloud service offerings powered by CA 3Tera AppLogic software and signs multi-year license agreement ...

Elsevier special issue on "Models and Algorithms for High-Performance Distributed Data Mining" to issue Call for Papers ...

IBM sets performance records with new eX5 servers ...

CA Technologies acquires IT consulting firm, Base Technologies ...

EMC helps Blue Diamond Solutions deliver Cloud based back-up ...

SAS to offer high-performance analytics on EMC Greenplum database appliance ...

IBM unveils next generation SmartCloud platform for business ...

SAS High-Performance Analytics on Teradata appliance extends analytic innovation to customers ...

Microsoft and Toyota announce strategic partnership on next-generation telematics ...

IBM unveils smart Cloud services and technologies for the enterprise ...

Latest CA Workload Automation release enables dynamic service and application automation across physical, virtual and Cloud infrastructures ...

Dell ups the performance bar on Powerhouse servers for mission critical workloads and applications ...

Electric Yellowstone - Conductivity image hints volcano plume is bigger than thought ...

Savtira Corporation selects Emerson Network Power for data centre infrastructure solution ...

New IBM software helps clients accelerate adoption and realize the benefits of Cloud computing ...

Intel Xeon processor E7 family delivers record-breaking performance, new security, reliability and energy efficiency features ...

PSSC Labs to showcase bionformatics supercomputer and other life science compute & storage solutions at BIO IT World ...

SAS OnDemand for Academics to be available at no cost for research ...

Altair Engineering announces the release of MindManager through the HyperWorks Partner Alliance ...

Joint European DCI Summer School to issue Call for Participation ...

EDGI demonstrates how to submit 10,000 jobs to a Volunteer Desktop Grid from within the European Grid Infrastructure ...

Blood vessel simulation probes secrets of brain ...

International research on controlled nuclear fusion: Bull is selected to provide the supercomputer to be installed in Rokkasho, Japan ...

EGI Technical Forum 2011 to be held in September in Lyon ...

Bull TrustWay Hardware Security Module now integrates with Oracle Advanced Security for Oracle Database 11g ...

4th IEEE International Conference on Utility and Cloud Computing to issue Call for Papers ...

EMC Isilon delivers breakthrough performance for big data ...

IBM teams with Akamai to accelerate applications across the web, and from the Cloud to the enterprise ...

IBM offers new opportunities to jump start Cloud computing for business partners and start-ups ...

IBM to deliver new optimized POWER7 products, inspired by Watson technology ...

Tate & Lyle Sugar's refining operations step into the Cloud with Virtustream and IBM ...

IBM and Sybase harness POWER7 for new mCommerce Appliance ...

Networking

HP helps VIVACOM integrate fixed and mobile networks for better services ...

Europe

e-IRG welcomes public comment on the e-IRG White Paper 2011 ...