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TACC adds software, support and expertise to broaden life science research: The Texas Advanced Computing Center (TACC), already a leader in high-performance computing (HPC), is broadening its computational biology programming, adding software, support and expertise to multiply the number of cutting-edge research projects carried out on Ranger and other HPC systems. Life scientists, including biologists, physicians, and biochemists, are increasingly using advanced computing to model life’s basic processes and interpret massive amounts of data. TACC is committed to helping them leverage the most capable resources for their research, shortening the path to discovery and inspiring new insights. In February, Dr. Michael Gonzales joined TACC as the Life Sciences Program Director. In his role, Gonzales is responsible for setting the center’s strategic direction in computational biology, developing the resources and services to support life sciences users, and leading collaborative research projects. His scientific efforts have been focused on various aspects of computational biology including high throughput genomics/proteomics and protein-ligand interactions. Prior to TACC, Gonzales worked for Apple Inc. where he headed up Scientific Computing for the Education division and recently received the Apple Science Innovator Award. 3D image of the GTP-binding alpha subunit of the heterotrimeric G protein, Gpa1, that couples to pheromone receptors in yeast. Gpa1 plays a critical role in the yeast signal transduction pathway. Models such as this help researchers to gain deeper understanding of how the process works and ultimately how similar pathways function in other organisms such as humans. “Not only does TACC want to serve the life science community and be involved in their research,” Gonzales said, “but we want to reach out to this community and bring them in.” Impactful biological research is already occurring at TACC, with scientists like Nathan Baker (Washington University) simulating the action of therapeutic nanoparticles in preparation for a next-generation cancer treatment, and Klaus Schulten (University of Illinois at Champaign-Urbana) modeling all 100 million atoms of a purple bacteria to better understand cellular structure. However, Gonzales believes that this is just the beginning, noting that throughout the life sciences, many researchers are not aware of what advanced computing, and specifically TACC, has to offer them. “TACC is not just about high-performance or supercomputing. There’s a wealth of infrastructure and expertise that we provide, from expert consulting services to advanced visualization technologies,” Gonzales noted. “When you consider all of what we have to offer, TACC becomes compelling to a diverse and broad base of scientific researchers.” This was certainly the case for Scott Stevens, assistant professor of molecular genetics and microbiology at The University of Texas at Austin, who is partnering with TACC on a pilot genome assembly project. “I heard from colleagues that UT Austin had some amazing computational power, but I never knew how to access it or what I might be able to do with it,” Stevens recalled. “Once I began asking the right questions of the right people, everything fell into place very quickly.” The genomics project brings together Stevens’ extensive laboratory-based knowledge of molecular biology and Gonzales’ experience with advanced computing. Exploiting the massive memory space and computing power of Ranger, the team is assembling the 1.3 billion base-pair genome of the Cyanidium caldarium, a eukaryotic microorganism that lives in the extreme conditions of deep-sea vents. The project represents the first time a genome has been assembled de novo at The University of Texas. “It’s like getting an Encyclopedia Britannica with all the words but none of them formed into any sentences, and you have to figure out how to put them together,” Gonzales explained. “Understanding where a given word fits into that encyclopedia is very complicated, but fortunately this is something that’s been wrestled with, and by using computers such as Ranger, we’re able to figure out how these things actually go together.” The project uses bioinformatics algorithms to locate and connect the overlapping segments of millions of short DNA sequences to reconstruct the organism’s entire genome. By sequencing the C. caldarium genome, Stevens hopes to understand how its proteins, so similar to our own, can withstand temperatures up to 600°F while human proteins melt at 110°F. This project is representative of the emerging class of computational problems in biology, where powerful, new laboratory tools create massive quantities of data, which require computational methods and resources to decipher. “Emerging technologies in genomics and proteomics easily produce many terabytes of data and require the computational infrastructure that TACC can provide,” Stevens said. Not only does TACC have capable systems, Gonzales says, its resources are available, easy to access, and best of all, free. For academic researchers to gain access to TACC’s systems and expertise, they simply need to submit a proposal stating their goals, how they expect to do their research, and why the work advances the body of science. “If you have a good scientific question, you can confidently assume you’ll get access to the systems," Gonzales divulged. “That’s pretty phenomenal, to be able to use Ranger, one of the most powerful supercomputers in the world, for your research.” Whereas physicists, astronomers and weather modelers have used advanced computing as a primary tool for decades, life scientists and biologists are less accustomed to applying simulation and computational modeling to their studies of cells, organisms and life-saving medicines. “This isn’t where they’ve been, it’s where they’re going,” Gonzales said. Which is why TACC is focused on engaging with life science researchers, discovering their needs, and making it easier for them to access the software, systems and expertise needed to accomplish their specific research. “Computational biology has developed into an amazing tool to help biologists of all kinds do things that were never possible before,” Stevens said. “From comparing millions of DNA sequences against each other, to rationally designing drugs which target particular proteins for curing diseases, computational biologists now have access to powerful tools that help them ask questions in new ways and achieve answers rapidly.” With a growing list of computational biology applications installed on Ranger, and the expertise to help novice users employ computer modeling and simulation tools with relative ease, Gonzales is confident that computational biology will flourish at TACC. “From cancer research, to basic aspects of life and disease, to new technologies that will enable us to do everything from detecting birth defects in unborn children to blood doping in the Tour de France,” Gonzales enumerated. “Biology is fundamentally important to our understanding of life and computers will continue to play an increasing role in those efforts.” Key applications on TACC systems available for Life Science Research:

• AutoDock4
• mpiBLAST
• R
• GROMACS
• Amber
• NAMD
• VMD

***************************************************** In the fall of 2008, TACC will begin training workshops to teach life scientists how to use advanced computing to its full potential. Online materials, describing TACC’s computational biology software and resources, will also be available at that time. To learn more, contact Michael Gonzales. Aaron Dubrow Texas Advanced Computing Center Science and Technology Writer