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You ought to be in pictures
January 2010
by Jeffrey Bouley  |  Email the author


PITTSBURGH—Using high-powered computing technology provided to them through an award from Armonk, N.Y.-based IBM, the University of Pittsburgh's McGowan Institute for Regenerative Medicine is borrowing similar techniques as used for special effects in films to study chronic hepatitis, liver cancer and other diseases through in silico models—with IBM noting that Pitt researchers "have begun building astonishingly realistic models of organs and diseases, and seeing molecular-level effects of drugs on them."  
By using computational techniques to simulate inflamed liver cells morphing into cancer—instead of creating imaginary characters to fill movie battle scenes, for example—the researchers are seeing not only how tumors develop, but how drugs or other interventions could affect disease progression.
According to IBM and Pitt, the level of in silico modeling being put to work through this corporate-academic pairing so closely mimics reality that it can produce images very similar to what pathologists see with tissues under the microscope. So far, the Pitt research team has already simulated liver tissue to study how a chronic hepatitis infection can lead to liver cancer, simulated lung tissues to study viral infection and chronic obstructive pulmonary disease, and simulated skin to study how patients with spinal cord injuries develop pressure ulcers.  
The project uses an IBM supercomputer—the IBM Power 575—which is put to work on such computationally-intensive workloads such as weather and climate modeling, physics, fluid dynamics and biological research. The project is part of a Shared University Research (SUR) award to Pitt from IBM, under which IBM will provide its hardware, software and services, and it ties into IBM's "A Smarter Planet" initiatives.  
Although Dr. Yoram Vodovotz, director of the Center for Inflammation and Regenerative Modeling at the McGowan Institute and a professor of surgery at Pitt's School of Medicine, is putting the IBM technology to work on a variety of disease modeling tasks, one of his core goals is to study the role of immune system-regulated inflammatory pathways in a variety of conditions. Inflammation, he notes, seems to lie at the root of many diseases affecting both industrialized and developing societies. The computer technology from IBM, both on the hardware and software sides, will simulate the multitude of molecular interactions that occur both in normal tissues and those affected by disease or illness.
"I think the world has come to a general consensus that inflammation plays large roles in many disease state that we are concerned with, from wound healing to trauma, neurodegenerative diseases to cancer, and more," Vodovotz says. "But while that may sound like we've found a simple connection between many diverse conditions, it's complicated, because inflammation is the ultimate 'no free lunch' paradigm. There is no simple way to handle one aspect of inflammation with a compensatory response that might cause additional problems elsewhere in the body."
Much of the work has been in a diagnostic and pathology-oriented vein, but Vodovotz and his team actually have three broad goals moving forward: personalized diagnostics, the creation of virtual clinical trials, and rational drug and device design.  
Computer modeling isn't new for the Pitt researchers, but the power of their equipment both for processing, analysis and storage has been far more limited than they would like over the years. Vodovotz says that the in silico modeling power he can bring to bear with the IBM technology can help him and his fellow Pitt researchers understand basic biological processes better, screen drugs computationally to determine their impact on the human body, focus in on the best intervention for a given disease, shorten the treatment evaluation process—and through all that, greatly cut the time and expense of getting drugs developed and onto the market.
"With these techniques, we could reduce the number of participants needed for human trials by creating some of them in silico, understand individual variation by exploring it in a digital world, and better visualize how the body responds when a drug or device enters it," Vodovotz explains. "We want to use this technology to apply more engineering-style principles instead of just brute-force testing our way through things or using reductionist thought patterns as to how a drug or process might work. Instead, we want to run as much as possible in simulation."  
This is not IBM's largest SUR Award, but it is in excess of $500,000, which makes it one the largest that IBM has awarded this year, notes Holli Haswell of the External Relations department of IBM Global Healthcare and Life Sciences. The SUR Award program is designed to, among other things, increase access to and successful use of IBM technologies for research and in curriculum, and it strives to connect researchers at universities with IBM Research, IBM Life Sciences, IBM Global Services and IBM's development and product labs.  
Speaking to the power of the SUR Awards to help advance research in biological, pharmaceutical and many other intensive research efforts, IBM Global University Programs Director Jim Spohrer remarks that he has passed by California's Moffett Federal Airfield numerous times in daily travel in Silicon Valley, and made note of the huge wind tunnel structures on the site.
"They are still used for research, but not very often anymore," he says, "because these are the kind of things we can do on computers now so much more efficiently and cost effectively."  
Spohrer says that out of the more than 5,000 university relationships IBM has formed worldwide, this one with Pitt stands out for it's wide-ranging potential, which is why this award is one of IBM's larger ones. "Each year, we're going to see more and more of what we do now in wet labs being done in silico," he says. "It's going to allow us to model the world more accurately and advance science more rapidly."

Smarter is cooler  
ARMONK, N.Y—The IBM Power 575 supercomputing node being put to use at the University of Pittsburgh for disease modeling and other purposes offers "a highly scalable system with extreme parallel processing performance and dense, modular packaging" for high-performance computing applications like weather and climate modeling, computational chemistry, physics, computer-aided engineering, computational fluid dynamics and petroleum exploration. With as many as 448 POWER6 processor cores per frame, each one running at 4.7 GHz and supported by up to 3.5 terabytes of memory per frame, the 32-core Power 575 supercomputing node is designed for speed and tuned for performance, notes IBM Global University Programs Director Jim Spohrer.   

But just as IBM's "A Smarter Planet" initiative is trying to make better use of resources and research by connecting industry with academia and academics with other academics across the planet, so too is it looking to make supercomputer a much "greener" process.
"One of the things I don't think gets enough press is that not only are we deploying these tremendously more powerful computing systems," Spohrer says, "but we're bringing down the problems of overheating and of energy usage, which is good for the environment and also bringing down the infrastructure cost of research."  
IBM touts that with the computing nodes injected with a chilled coolant to enable peak performance, "this system is a supersonic race car on the IT highway."
Reportedly, this Power 575 system uses a first-of-its-kind system in which water-chilled copper plates are located above each microprocessor, continually removing heat from the electronics. IBM says that the Power 575 can reduce the number of air-conditioning units required in a typical customer configuration of clusters by more than 80 percent, and IBM scientists estimate that water can be up to 4,000-times more effective in cooling computer systems than air.
Code: E011003



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