iSGTW - International Science Grid This Week
iSGTW - International Science Grid This Week

Home > iSGTW - 17 June 2009

Issue 129: iSGTW 17 June 2009


Grid-Enabled virus hunting

Researchers use distributed computing resources from the TeraGrid and the Open Science Grid to make sequence analysis faster and easier.

DNA sequencing and sequence analysis happens daily in many biological sciences laboratories, but analyzing large sets of genetic data increasingly requires computing resources beyond the capabilities of most labs.

The search for the best hardware and software led Eric Delwart, a professor of laboratory medicine at the University of California, San Francisco, and a senior investigator at the Blood Systems Research Institute, and Chunlin Wang, a research associate at the Stanford University Genome Technology Center, to the Renaissance Computing Institute's (RENCI) Engagement Team and then to the distributed computing resources of the TeraGrid and the Open Science Grid (OSG).

Delwart works with Wang to identify new viruses. The team uses a technique called massively parallel pyrosequencing, which can determine sequences for millions of DNA fragments using high-throughput computing. The resulting DNA sequences are then compared to all the sequences in public sequence databases to identify viral fingerprint sequences. One single sequencing reaction generates massive volumes of data that can take months, even years, to analyze on a small-scale computing cluster.

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/ Swine flu and the grid: A researcher's view

The emergence of Swine Flu may be an opportunity for the grid to contribute to the international public health response.
By providing a collaborative environment, computing power to screen potential drugs and a means to dynamically process new information, the grid can help researchers rapidly identify a new virus strain and thus quantify an outbreak and monitor its evolution, says a researcher.

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NCSA’s Blue Waters  

/ Coming: Sustained petascale computing for open science

The first sustained petascale computing system for “open” science — science done using open source tools — is expected to come fully online in 2011. Called Blue Waters, it will be capable of performing one million billion operations per second and will open up even greater opportunities to address some of most challenging problems in science and engineering.

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Link of the week

/From The Economist: Sensors and sensitivity

 Engineers, biologists, sociologists and aid-workers are now building systems that use handsets to sense, monitor and even predict population movements, environmental hazards and public-health threats.

Some computer scientists look forward to the day when mobile phones and sensors can provide a central nervous system for the entire planet . . .

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Image of the week

A physicist sketches science in the style of an old master


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 iSGTW 22 December 2010

Feature – Army of Women allies with CaBIG for online longitudinal studies

Special Announcement - iSGTW on Holiday

Video of the Week - Learn about LiDAR


NeHC launches social media

PRACE announces third Tier-0 machine

iRODS 2011 User Group Meeting

Jobs in distributed computing


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 iSGTW Blog Watch

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 Mark your calendar

December 2010

13-18, AGU Fall Meeting

14-16, UCC 2010

17, ICETI 2011 and ICSIT 2011

24, Abstract Submission deadline, EGI User Forum


January 2011

11, HPCS 2011 Submission Deadline

11, SPCloud 2011

22, ALENEX11

30 Jan – 3 Feb, ESCC/Internet2


February 2011

1 - 4, GlobusWorld '11

2, Lift 11

15 - 16, Cloudscape III

More calendar items . . .


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