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Primeur weekly 2012-08-06

The Cloud

Oracle buys Xsigo ...

M2M player Arkessa chooses Telecloud, the data centre Cloud ...

Cavium unveils Project Thunder to reshape the next generation Cloud and data centre ...

Rackspace Open Cloud offers easily scalable computing and freedom from vendor lock-in ...

Transactional processing, secure in the Cloud - now a reality with TransCertain and RACE ...

Desktop Grids

Collaborative computing, pioneered at University of Wisconsin-Madison, helped drive LHC analysis ...

EuroFlash

Visualization Sciences Group announces acquisition of amira 3D visualization and analysis software for life sciences and bio-medical data ...

MPI-3.0 public draft and call for comments ...

Getting started with Allinea DDT tutorials ...

Rothamsted Research increases its DNA sequencing and analysis capability by adding the new Active Motif TimeLogic Biocomputing platform ...

USFlash

Cray reports strong second quarter 2012 results ...

New supercomputer bolsters world's biggest radio telescope ...

University of Rochester inaugurates new era of health care research ...

Tokyo Institute of Technology and Astellas: start of joint drug discovery research for neglected tropical diseases ...

Mapping the future of climate change in Africa ...

Massive data for miniscule communities ...

HP boosts application performance with HP 3PAR solid state technology ...

California Institute of Technology selects Oracle's StorageTek Tape Storage to archive and access petabytes of scientific research data ...

A new high performance and fault-tolerant datacenter network for modular datacenters was proposed ...

FEI buys 3D Visualization Software Company ...

Networcsim hoping to broaden wireless revolution ...

Massive data for miniscule communities

1 Aug 2012 East Lansing - It's relatively easy to collect massive amounts of data on microbes. But the files are so large that it takes days to simply transmit them to other researchers and months to analyze once they are received. Researchers at Michigan State University (MSU) have developed a new computational technique, featured in the current issue of theProceedings of the National Academy of Sciences, that relieves the logjam that these "big data" issues create.

Microbial communities living in soil or the ocean are quite complicated. Their genomic data is easy enough to collect, but their data sets are so big that they actually overwhelm today's computers. C. Titus Brown, MSU assistant professor in bioinformatics, demonstrates a general technique that can be applied on most microbial communities.

The interesting twist is that the team created a solution using small computers, a novel approach considering most bioinformatics research focuses on supercomputers, C. Titus Brown said.

"To thoroughly examine a gram of soil, we need to generate about 50 terabases of genomic sequence - about 1,000 times more data than generated for the initial human genome project", stated C. Titus Brown, who co-authored on the paper with Jim Tiedje, University Distinguished professor of microbiology and molecular genetics. "That would take about 50 laptops to store that much data. Our paper shows the way to make it work on a much smaller scale."

Analyzing DNA data using traditional computing methods is like trying to eat a large pizza in a single bite. The huge influx of data bogs down computers' memory and causes them to choke. The new method employs a filter that folds the pizza up compactly using a special data structure. This allows computers to nibble at slices of the data and eventually digest the entire sequence. This technique creates a 40-fold decrease in memory requirements, allowing scientists to plow through reams of data without using a supercomputer.

C. Titus Brown and Jim Tiedje will continue to pursue this line of research, and they are encouraging others to improve upon it as well. The researchers made the complete source code and the ancillary software available to the public to encourage extension.

"We want this programme to continue to evolve and improve", C. Titus Brown stated. "In fact, it already has. Other researchers have taken our approach in a new direction and made a better genome assembler."
Source: Michigan State University

Back to Table of contents

Primeur weekly 2012-08-06

The Cloud

Oracle buys Xsigo ...

M2M player Arkessa chooses Telecloud, the data centre Cloud ...

Cavium unveils Project Thunder to reshape the next generation Cloud and data centre ...

Rackspace Open Cloud offers easily scalable computing and freedom from vendor lock-in ...

Transactional processing, secure in the Cloud - now a reality with TransCertain and RACE ...

Desktop Grids

Collaborative computing, pioneered at University of Wisconsin-Madison, helped drive LHC analysis ...

EuroFlash

Visualization Sciences Group announces acquisition of amira 3D visualization and analysis software for life sciences and bio-medical data ...

MPI-3.0 public draft and call for comments ...

Getting started with Allinea DDT tutorials ...

Rothamsted Research increases its DNA sequencing and analysis capability by adding the new Active Motif TimeLogic Biocomputing platform ...

USFlash

Cray reports strong second quarter 2012 results ...

New supercomputer bolsters world's biggest radio telescope ...

University of Rochester inaugurates new era of health care research ...

Tokyo Institute of Technology and Astellas: start of joint drug discovery research for neglected tropical diseases ...

Mapping the future of climate change in Africa ...

Massive data for miniscule communities ...

HP boosts application performance with HP 3PAR solid state technology ...

California Institute of Technology selects Oracle's StorageTek Tape Storage to archive and access petabytes of scientific research data ...

A new high performance and fault-tolerant datacenter network for modular datacenters was proposed ...

FEI buys 3D Visualization Software Company ...

Networcsim hoping to broaden wireless revolution ...