July 18, 2012
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 31st 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.
The Xeon Phi coprocessor might be the new kid on the high performance block, but out of all first-rate kickers of the Intel tires, the Texas Advanced Computing Center (TACC) got the first real jab with its new top ten Stampede system.We talk with the center's Karl Schultz about the challenges of programming for Phi--but more specifically, the optimization...
Read more...
Although Horst Simon was named Deputy Director of Lawrence Berkeley National Laboratory, he maintains his strong ties to the scientific computing community as an editor of the TOP500 list and as an invited speaker at conferences.
Read more...
Supercomputing veteran, Bo Ewald, has been neck-deep in bleeding edge system development since his twelve-year stint at Cray Research back in the mid-1980s, which was followed by his tenure at large organizations like SGI and startups, including Scale Eight Corporation and Linux Networx. He has put his weight behind quantum company....
Read more...
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
04/15/2013 | Bull | “50% of HPC users say their largest jobs scale to 120 cores or less.” How about yours? Are your codes ready to take advantage of today’s and tomorrow’s ultra-parallel HPC systems? Download this White Paper by Analysts Intersect360 Research to see what Bull and Intel’s Center for Excellence in Parallel Programming can do for your codes.
In this demonstration of SGI DMF ZeroWatt disk solution, Dr. Eng Lim Goh, SGI CTO, discusses a function of SGI DMF software to reduce costs and power consumption in an exascale (Big Data) storage datacenter.
The Cray CS300-AC cluster supercomputer offers energy efficient, air-cooled design based on modular, industry-standard platforms featuring the latest processor and network technologies and a wide range of datacenter cooling requirements.