HPCwire: Aussie Supercomputer Simulates Common Cold's Susceptibility to New Drug

King Abdullah University of Science and Technology

Since 1986 - Covering the Fastest Computers
in the World and the People Who Run Them

Translation Disclaimer

Subscribe | Sign In

Tabor Communications
Corporate Video

Leading HPC
Solution Providers

July 18, 2012

Aussie Supercomputer Simulates Common Cold's Susceptibility to New Drug

Robert Gelber

The human rhinovirus, otherwise known as the common cold, is usually a fairly minor inconvenience for its human hosts. But the symptoms are far more serious for those suffering from asthma and chronic obstructive pulmonary disease (COPD). Today roughly 70 percent of heightened asthma symptoms are linked to the common cold. Over 50 percent of those affected eventually require hospitalization. It is also responsible for sending more than 35 percent of COPD sufferers to hospitals each year.

To help the at-risk population, Biota Holdings Ltd., a Melbourne-based company is developing an antiviral drug. This has led members from St. Vincent’s Institute of Medical Research (SVI) and the University of Melbourne to research how the drug works against the rhinovirus.

In a press release describing the work, scientists are using supercomputing simulations as a basis for revealing the drug’s efficacy. Professor Michael Parker, who leads the research team, explained the basic mechanics behind the new compound. “Our recently published work with Biota shows that the drug binds to the shell that surrounds the virus, called the capsid. But that work doesn’t explain in precise detail how the drug and other similar acting compounds work,” he said.

Part of the team’s study involved creating a 3D model of the rhinovirus. It was simulated using the recently deployed Avoca supercomputer at Melbourne University. An IBM Blue Gene/Q machine, the system has 65,536, 1.6GHz power cores with 65 terabytes of memory. At 838 peak teraflops (690 teraflops Linpack), Avoca is the fastest computer in Australia and ranks 31^st on the June 2012 TOP500 list.

Parker said that supercomputers like Avoca have enabled scientists to study how drugs function at a molecular level. The new system can now simulate the entire rhinovirus in useful time frames, which in turn can accelerate the discovery and development of new treatments. Prior to the Avoca’s installation, researchers only had the capability to run simulations on portions of the virus.

If the research proves successful, it could reduce the lethality of the common cold for at-risk populations while reducing associated medical costs. Dr. John Wagner, the manager at IBM’s Research Collaboratory for Life Sciences in Melbourne, noted that simulations like this are going to drive life science research moving forward. “This is the way we do biology in the 21st Century,” he said.

Share Options

Subscribe

Subscribe to HPCwire

Discussion

There are 0 discussion items posted.

Join the Discussion

Become a Registered User Today!

Registered Users Log in join the Discussion

RSS Feeds

Feeds by Topic

Feeds by Industry

Feeds by Content Type

Subscribe to All Content

All

July 20, 2012

July 19, 2012

July 18, 2012

July 17, 2012

July 16, 2012

July 13, 2012

July 12, 2012

July 11, 2012

July 10, 2012

Feature Articles

Too Big to FLOP?

At the cutting edge of HPC, bigger has always been seen as better and user demand has been the justification. However, as we now grapple with trans-petaflop machines and strive for exaflop ones, is evidence emerging that contradicts these notions? Might computers be getting too big to effectively serve up those FLOPS?
Read more...

Researchers Squeeze GPU Performance from 11 Big Science Apps

In a report published this week, researchers documented that GPU-equipped supercomputers enabled application speedups between 1.4x and 6.1x across a range of well-known science codes. While those results aren't the order of magnitude performance increases that were being bandied about in the early days of GPU computing, the researchers were encouraged that the technology is producing consistently good results with some of the most popular HPC science applications in the world.
Read more...

Intel Expands HPC Collection with Whamcloud Buy

Intel Corporation has acquired Whamcloud, a startup devoted to supporting the open source Lustre parallel file system and its user community. The deal marks the latest in a line of high performance computing acquisitions that Intel has made over the past few years to expand its HPC footprint.
Read more...

Read more HPCwire features...

Tackling the Data Deluge: File Systems and Storage Technologies

06/25/2012 | NetApp | A single hour of data collection can result in 7+ million files from just one camera. Collection opportunities are limited and must be successful every time. As defense and intelligence agencies seek to use the data collected to make mission-critical battlefield decisions, there’s greater emphasis on smart data and imagery collection, capture, storage and analysis to drive real-time intelligence. The data gathered must accurately and systematically be analyzed, integrated and disseminated to those who need it – troops on the ground. This reality leads to an inevitable challenge – warfighters swimming in sensors, drowning in data. With the millions, if not billions, of sensors providing all-seeing reports of the combat environment, managing the overload demands a file system and storage infrastructure that scales and performs while protecting the data collected. Part II of our whitepaper series highlights NetApp’s scalable, modular, and flexible storage solution to handle the demanding requirements of sophisticated ISR environments.

View the White Paper Library

Michael Wolfe Webinar: PGI Accelerator with OpenACC

Join Michael for a look at the first PGI Accelerator Fortran and C compilers to include comprehensive support for OpenACC, the new open standard for programming accelerators using compiler directives.