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iSGTW Feature - Where are they now?

Feature - Where are they now?


Interconnected computers for high performance operations call for strong interoperability.
Image courtesy of cordis.europa.eu

Updates from the three projects covered in iSGTW's inaugural issue, 16 November 2006.

Building the global grid

ISGTW led its first issue with a feature on the possibility of and progress toward achieving one seamless global grid. At the time of writing, basic interoperation between Open Science Grid and Enabling Grids for E-sciencE had been achieved, according to Laurence Field of EGEE.

"Scientists using either infrastructure can now submit jobs to both and copy data between the infrastructures," Field said. "And if another grid interoperates with either, they'll see the other grid's resources. Through activities like these we hope to build up a homogenous grid landscape."

Where are they now?

Morris Riedel of the Jülich Supercomputing Centre in Germany, and chair of the Grid Interoperation Now (GIN) group within the Open Grid Forum, says that since then, members of GIN have tested emerging common open standard implementations deployed on production infrastructures to see if they can be used in real multi-grid scientific use cases.

Using lessons learned from this work, GIN has defined an interoperability reference model (IRM) that profiles mature standards in job and data management and security that can be deployed on production infrastructures to enable interoperability. This model represents a trimmed-down and more specific version of the Open Grid Services Architecture (OGSA), and thus represents one mid-term milestone towards full OGSA conformance as a long-term goal.


Exploring the Gravitational Wave (and Grid) Universe

Two years ago, the Laser Interferometer Gravitational-Wave Observatory (LIGO) was on the computationally-intensive hunt for gravitational waves and the perfect grid. Theories predict one gravitational-wave event every 10 years. With the help of the LIGO Data Grid in partnership with the Open Science Grid, LIGO diligently searched the skies for these the raw signatures of a gravitational wave.

Last May, iSGTW reported on LIGO's Einstein@Home volunteer computing project to attract CPU power to their search for a gravitational signature from spinning neutron stars. Einstein@HOME had reached one million BOINC credits a day, and had started running opportunistically on Open Science Grid resources, which led to significantly increased throughput.

Where are they now?

While the collaboration installs the Enhanced LIGO hardware to enhance sensitivity for a new science run in 2009, LIGO scientists are analyzing 2007 "coincident" data from five geographically-separated detectors. Since May of this year, most days see over 1500 jobs on OSG, with a few days in the 5000's or above - a tiny fraction of what happens on Einstein@home; the recent average BOINC credit (a daily measure) is almost 13 million, second only to SETI@home!

LIGO expects to collect a year's worth of data during the new run and will look at about 10 times the volume of the universe. This will be a precursor to yet the next generation "Advanced LIGO" instruments.


Image courtesy of cordis.europa.eu

WISDOM vs. Malaria (round two)

In silico, in vitro, in vivo

WISDOM harnesses the power of grid computing to look for drug candidates. In 2005, the first data challenge targeted a specific enzyme from the life cycle of the malaria-causing parasite. In a second data challenge in 2006, with the support of the EGEE and several related European grid projects, WISDOM tested up to 150,000 compounds per hour on up to 5,000 computers around the world.

In March 2007 iSGTW reported that WISDOM had tested 4.3M potential malarial medicines during this second phase, and analyzed possible docking arrangements between drug compounds and target proteins of the malaria parasite.

In May of this year iSGTW reported that after having screened a million molecules in silico, the team selected 30 promising candidates to undergo evaluation in a wet lab. Almost all 30 successfully inhibited the enzyme, and hence the parasite.

Where are they now?

Ten of these 30 compounds have advanced to the next stage: testing in live parasite cultures for toxicity to parasite cells (while sparing human cells) and pharmacological potential. So far, these properties have not reached adequate levels in the selected compounds, so scientists are synthesizing related compounds, aiming to boost the levels.

Meanwhile, two more malaria targets are moving to the laboratory for testing.

-Anne Heavey, iSGTW

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