Visit additional Tabor Communication Publications
June 07, 2012
DALLAS, TX, June 6 -- When chemotherapy fails to halt the spread of cancer, it is typically because new super cells develop resistance to the chemotherapy. Instead of dying off, the cells reject the medicine, are able to pump it out and continue to thrive and reproduce.
Scientists have long tried to find a drug to combat these super cells. Now biochemists Pia Vogel and John Wise in the Department of Biological Sciences in Dedman College are using SMU’s supercomputer to tackle the problem. Vogel and Wise are searching for a drug that will shut off the cancer cell “sump pump” so that chemotherapy can once again be effective. They are collaborating with other researchers at SMU’s Center for Drug Discovery, Design and Delivery.
“This is a desperate situation for people whose cancer returns in an aggressive state,” says Wise, a research associate professor. “We don’t want to knock out this sump-pump system permanently, but would like to find a drug that will inhibit the pump, then allow the body to return to its normal state.”
“If we could search through millions of compounds we could potentially find one that could ‘throw a stick’ in the sump-pump mechanism,” says Vogel, an associate professor. Because testing each one in a lab would be too costly and take a lifetime, they adopted a faster method.
Using simulation software and a computational model of the “sump-pump” protein called P-glycoprotein, they screen potential compounds digitally through SMU’s High Performance Computing (HPC) system. With the computational model, Wise and Vogel can observe on a computer screen how digital compounds are absorbed onto and into the P-glycoprotein model. Compounds that stick or bind instead of being pumped out have potential as an effective drug.
Creating the P-glycoprotein model was not easy. The structures of P-glycoprotein in mice and bacteria are well understood. But human P-glycoprotein remains a mystery and is highly unstable in the lab. Wise designed the computational model by deducing and inferring characteristics from what is known about human P-glycoprotein.
So far, the researchers have screened millions of digital compounds, a process that took 7.55 million computational hours on the HPC. They’ve discovered more than 300 potentially effective compounds. With a team of students, the scientists have tested 30 of those 300 compounds in the lab and found several that inhibit the protein.
Wise and Vogel also are working with their colleague and Associate Professor Robert Harrod to test a multidrug resistant line of cancer cells to see if the drugs again can make the cells susceptible to chemotherapy.
Source: Southern Methodist University
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...
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.
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....
May 16, 2013 |
When it comes to cloud, long distances mean unacceptably high latencies. Researchers from the University of Bonn in Germany examined those latency issues of doing CFD modeling in the cloud by utilizing a common CFD and its utilization in HPC instance types including both CPU and GPU cores of Amazon EC2.
May 15, 2013 |
Supercomputers at the Department of Energy’s National Energy Research Scientific Computing Center (NERSC) have worked on important computational problems such as collapse of the atomic state, the optimization of chemical catalysts, and now modeling popping bubbles.
May 10, 2013 |
Program provides cash awards up to $10,000 for the best open-source end-user applications deployed on 100G network.
May 09, 2013 |
The Japanese government has revealed its plans to best its previous K Computer efforts with what they hope will be the first exascale system...
May 08, 2013 |
For engineers looking to leverage high-performance computing, the accessibility of a cloud-based approach is a powerful draw, but there are costs that may not be readily apparent.
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.