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Primeur weekly 2015-03-23

Special

University of Kent team to work on protocol independent federated identity management in OpenStack ...

From Cloud federation to general federation management ...

The Cloud

EGI.eu is looking for an Operations Officer ...

VMware announces general availability of VMware vSphere 6, VMware Integrated OpenStack and VMware Virtual SAN 6 ...

VMware Announces General Availability of vCloud Air in Germany ...

HP helps TNT future-proof business through IT transformation ...

EuroFlash

ISC 2015 keynotes focus on latest innovation and future challenges ...

Allinea releases CUDA 7 debugging support and extends performance tools to CUDA ...

Allinea delivers OpenPOWER debugging ...

PRACE completes first phase of Pre-Commercial Procurement ...

Superfast computers a step closer as a silicon chip's quantum capabilities are improved ...

USFlash

SDSC researchers win NVIDIA's 2015 Global Impact Award ...

Researchers rethink how our feathered friends evolved ...

SDSC/UCSD study uncovers mechanisms of cancer-causing mutations ...

Supermicro debuts new NVIDIA Tesla GPU SuperServers optimized for extreme parallel computing ...

HP brings scalable, high-performance storage solutions within reach of more midsized businesses ...

New optical materials break digital connectivity barriers ...

Scientists invent new way to control light, critical for next gen of super fast computing ...

Supercomputers help solve puzzle-like bond for biofuels ...

NVIDIA unveils Digits DevBox supercomputer aimed at researchers ...

Brookhaven presents Big Data pilot projects at Supercomputing Conference ...

Tohoku University and Fujitsu succeed in real-time flood analysis using supercomputer-based high-resolution tsunami modelling ...

Use of reclaimed water fuels decrease at Los Alamos ...

HP helps small businesses gain a competitive edge with new compute platforms ...

Data structures influence speed of quantum search in unexpected ways ...

Researchers rethink how our feathered friends evolved


16 Mar 2015 San Diego - A recently published global genome study that used the data-intensive Gordon supercomputer at the San Diego Supercomputer at the University of California, San Diego, has researchers rethinking how avian lineages diverged after the extinction of the dinosaurs.

The four-year project, called the Avian Genome Consortium and published in the journalScience, resulted in a new family "tree" for nearly all of the 10,000 species of birds alive today by comparing the entire DNA codes (genomes) of 48 species as varied as parrot, penguin, downy woodpecker, and Anna's hummingbird. The massive undertaking, started in 2011, involved more than 200 researchers at 80 institutions in 20 countries, with related studies involving scientists at more than 140 institutions worldwide.

The genome-scale phylogenetic analysis of the 48 bird species considered approximately 14,000 genes. This presented computational challenges not previously encountered by researchers in smaller-scale phylogenomic studies based on analyses of only a few dozen genes. The inclusion of hundreds of times more genetic data per species allowed the researchers to realize the existence of new inter-avian relationships.

"Characterization of genomic biodiversity through comprehensive species sampling has the potential to change our understanding of evolution", wrote Erich Jarvis, associate professor of neurobiology at the Howard Hughes Medical Institute at Duke University and the study's principal investigator, in an introduction to a special issue of the journalSciencecontaining eight papers from the study. An additional 20 papers generated by the study were simultaneously published in other journals.

"For 50 species, more than 10 to the power of 76 possible trees of life exist. Of these, the right one has to be found", stated Andre J. Aberer, with the Heidelberg Institute for Theoretical Studies (HITS), in a news release at the time of the study's publication inScience. "For comparison: About 10 to the power of 78 atoms exist in the universe."

Many of the computations were done on SDSC's Gordon supercomputer by Andre J. Aberer with the assistance of SDSC Distinguished Scientist Wayne Pfeiffer. They ran a new code called ExaML (Exascale Maximum Likelihood) to infer phylogenetic trees using Gordon soon after it debuted in 2012 as one of the 50 most powerful supercomputers in the world.

Developed by Alexandros Stamatakis, head of the Scientific Computing Group at HITS, ExaML couples the popular RAxML search algorithm for inference of phylogenetic trees using maximum likelihood with an innovative MPI parallelization approach. This yields improved parallel efficiency, especially on partitioned multi-gene or whole-genome data sets.

"I had previously collaborated with Alexis on improving the performance of RAxML", stated Wayne Pfeiffer. "He described the goals of the Avian Genome Consortium, and we agreed that Gordon, with its just-released fast processors, could provide much of the computer time needed for this ambitious project. In the end, more than 400,000 core hours of computer time were consumed on Gordon."

"After doing initial analyses on our institutional cluster, we rapidly realized that comprehensive analysis of the more challenging data sets being considered would require supercomputer resources", stated Andre J. Aberer. "Access to Gordon was thus invaluable for achieving results in a timely manner."

In all, high-performance computing (HPC) resources at nine supercomputer centres were used to analyze the complete genomes because of the scope of the undertaking. In addition to Gordon, several other U.S.-based supercomputers that are or have been part of the National Science Foundation's eXtreme Science Engineering and Discovery Environment (XSEDE) were used: Ranger, Lonestar, and Stampede at the Texas Advanced Computing Center (TACC) at the University of Texas at Austin; and Nautilus at the National Institute of Computational Sciences (NICS) at the University of Tennessee.

Resolving the timing and phylogenetic relationships of birds is important not only for comparative genomics, but can also inform about human traits and diseases, according to the researchers. For example, the study included vocal-learning species - such as parrots and hummingbirds - which can serve as models for spoken language in humans and may prove useful for insights into speech disorders.
Source: San Diego Supercomputer Center - SDSC

Back to Table of contents

Primeur weekly 2015-03-23

Special

University of Kent team to work on protocol independent federated identity management in OpenStack ...

From Cloud federation to general federation management ...

The Cloud

EGI.eu is looking for an Operations Officer ...

VMware announces general availability of VMware vSphere 6, VMware Integrated OpenStack and VMware Virtual SAN 6 ...

VMware Announces General Availability of vCloud Air in Germany ...

HP helps TNT future-proof business through IT transformation ...

EuroFlash

ISC 2015 keynotes focus on latest innovation and future challenges ...

Allinea releases CUDA 7 debugging support and extends performance tools to CUDA ...

Allinea delivers OpenPOWER debugging ...

PRACE completes first phase of Pre-Commercial Procurement ...

Superfast computers a step closer as a silicon chip's quantum capabilities are improved ...

USFlash

SDSC researchers win NVIDIA's 2015 Global Impact Award ...

Researchers rethink how our feathered friends evolved ...

SDSC/UCSD study uncovers mechanisms of cancer-causing mutations ...

Supermicro debuts new NVIDIA Tesla GPU SuperServers optimized for extreme parallel computing ...

HP brings scalable, high-performance storage solutions within reach of more midsized businesses ...

New optical materials break digital connectivity barriers ...

Scientists invent new way to control light, critical for next gen of super fast computing ...

Supercomputers help solve puzzle-like bond for biofuels ...

NVIDIA unveils Digits DevBox supercomputer aimed at researchers ...

Brookhaven presents Big Data pilot projects at Supercomputing Conference ...

Tohoku University and Fujitsu succeed in real-time flood analysis using supercomputer-based high-resolution tsunami modelling ...

Use of reclaimed water fuels decrease at Los Alamos ...

HP helps small businesses gain a competitive edge with new compute platforms ...

Data structures influence speed of quantum search in unexpected ways ...