The Real <I>Fantastic Voyage</I>: Bioinformatics
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New visualization tools are revolutionizing life sciences. Background It could be a scene from Fantastic Voyage: A team of researchers travel deep inside a human body, moving slowly around the edge of a cell. They watch, fascinated, as an enzyme approaches the cell membrane, attaches itself to a receptor molecule, and inserts its chemical payload. This isn't science fiction—in fact, it's business as usual at the University of Calgary's Sun Center for Visual Genomics. The university's immersive virtual reality environment, like more than 100 similar facilities around the world, provides an important new tool for life sciences researchers. From ribosomal RNA analysis to osteoporosis research, the University of Calgary's CAVE Automatic Virtual Environment (CAVE) offers something even the most powerful supercomputers cannot provide: a new way to look at life. Challenge Immersive visualization technology is barely a decade old. Yet it has already revolutionized the way scientists and researchers work in fields from automotive design to weather prediction. In the life sciences, immersive visualization tools are especially important, as researchers work to analyze increasingly large and complex data sets. Gene expression and proteomics data, for example, require four-dimensional modeling tools to detect subtle spatial and temporal relationships, rather than the much more obvious changes visible in traditional two-dimensional models. And within the rapidly growing field of functional genomics, researchers are using facilities such as the University of Calgary's CAVE to build working, multi-dimensional models of cells, tissues, organs, and even entire organisms. "Visualization tools are unbelievably helpful when you're dealing with vast arrays of unstructured data," says Dr. Stefan Unger, business development manager for Sun Microsystems' Computational Biology Special Interest Group. "It's far more efficient to view this type of data in an immersive environment, because it provides an intuitive way to detect very subtle relationships." Solution In many ways, CAVE is a typical example of an advanced immersive visualization system. The system includes four high-resolution stereo projection displays supplied and installed by Fakespace Systems. Three of the displays point at the walls of the 2.4-cubic-meter CAVE enclosure, creating a 270-degree surrounding view; the fourth is aimed at the floor. The system also uses a Sun Fire 6800 server equipped with 20 UltraSPARC III processors and four Sun Expert3D graphics accelerators, along with a 5-terabyte disk array and 20 terabytes of additional near-line tape storage. In order to achieve a realistic effect, the user wears electronic shutter glasses that create rapidly changing, alternate left- and right-eye views. The user's brain unconsciously fuses these images into a single view, creating a highly realistic, immersive visual experience that mimics the way humans view the "real" world. The user also operates a joystick-like device and can manipulate objects in real time. Yet the University of Calgary's CAVE differs from its counterparts in one important way: its groundbreaking use of the Java 3D extension. Other CAVE systems rely on proprietary programming interfaces; developers must create visualization objects on the same hardware that will run it. The Calgary CAVE, however, uses Java 3D application programming interface: a relatively simple, platform-independent programming language that has enjoyed growing acceptance among life sciences researchers. Results The Calgary CAVE is the first facility in the world to use the Java 3D extension, which allows developers to build Java 3D objects on almost any system—all they need is a pair of stereo glasses and a flat panel display to get a general idea of how their simulation will work in the CAVE. As a result, researchers can prepare their visualization experiments before they ever see the CAVE facility, rather than competing for precious in-house development resources. "This was a crucial breakthrough," says Dr. Christoph Sensen, professor of biochemistry and molecular biology. "Until Java 3D came along, you had to sit inside the CAVE and program. We would have spent most of our time programming, rather than working with finished products." According to Sensen, Java technology's role as a lingua franca within bioinformatics provides additional advantages. "Over the past few years, Java has become the single most important programming language in bioinformatics," he says. "It's the first language students learn today, it's free for end users, and it's available on almost every platform." University of Calgary Snapshot
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