The Delaware Biotechnology Institute and Silicon Graphics Inc. (SGI) were joint hosts for a Life Science Executive Summit on “Delivering Technology Leadership for Life Sciences” held Thursday, Oct. 3.
The summit featured a distinguished roster of researchers from leading pharmaceutical companies, bioinformatics organizations and universities, and was attended by more than 100 scientists and technical staff.
University of Delaware:
Accelerating Life Sciences Research through Visualization
In the Visualization Studio of the Delaware Biotechnology Institute (DBI), at the University of Delaware, a class of eight graduate students wearing stereo glasses is seated before a 100-square-foot screen in a black room. They are interacting with a room-sized display of a three-dimensional protein. As the professor manipulates the molecule, the students ask for changes in orientation, discuss the protein's structure, build on each other's observations, and point out bonding sites. With this 3D visualization, powered by an SGI® Onyx® 3200 supercomputer, they will achieve more in minutes than they could achieve in many hours of independent work at their individual workstations.
DBI: A New Interdisciplinary Research Facility
The 72,000-square-foot Delaware Biotechnology Institute is part of a statewide initiative whose purpose is to establish Delaware as a center of life sciences. The facility and its 40 scientific laboratories are designed to accommodate 170 faculty and student researchers. DBI serves as an incubator for start-up companies specializing in life sciences.
Research and education at the institute is focused on agriculture, human health, marine ecosystems, and biomaterials. Faculty, students, and professionals working at the institute are skilled in molecular biology, genomics, proteomics, structural biology, and computational biology.
"The Delaware Biotechnology Institute, a research facility designed for scientists by scientists, serves as a reminder and a very real symbol of a partnership between the state of Delaware, higher education institutions, and the private sector," Dr. David P. Roselle, president of the University of Delaware, says. "This facility demonstrates, better than any words could do, the promise and the benefit that can come to us all when these three entities work together. We are especially pleased to be working with SGI, a company with an international reputation for its leading-edge technologies."
SGI: Adding the Power of Immersive Visualization
DBI's state-of-the-art instrumentation is grouped in core centers run by on-site professionals. A major core center is the new Visualization Studio. SGI Professional Services managed the installation of this SGI® Reality CenterTM system, which includes a 15x8-foot FakeSpace® rear-projection screen. A six-processor Onyx 3200 visualization supercomputer with two graphics pipes drives a pair of Mirage 2000 projectors to deliver an edge-blended image with a total resolution of approximately 2500x1024 pixels.
Prof. Yong Duan of UD's Department of Chemistry and Biochemistry uses visualization tools to study peptide-folding processes in amino acids. Duan's folding simulations, which depict events that take just a few nanoseconds in the real world, may require a computer run of five days or more on a single-processor computer. Duan pauses regularly during the simulation to capture the current configuration of the folding peptide. He then combines these captured positions into a movie that will be displayed in the near future in immersive stereo on the SGI® Onyx® family system. It is striking and highly informative to watch, for instance, a 16-amino-acid straight-chain molecule fold, contort, and gradually assume a helix formation.
A few blocks away on campus, Dr. Guang Gao, professor of Electrical and Computer Engineering and director of DBI's Center for Bioinformatics, uses the output of a 2-CPU Onyx family system, displayed on a 4-by-6-foot FakeSpace® screen, to study technology that will, for example, enable scientists and surgeons to plan an operation jointly by interacting with the same medical image in separate immersive environments. SGI® OpenGL VizserverTM software will play a key role in this development.
Visualization Accelerates Bioinformatics
"Many investigators are using readily available tools like BLAST to solve comparative genomics questions," Gao says. "Over the next decade we will be looking for other ways to predict what organisms will do, and that is where visualization will play a dramatic role." Praveen Thiagarajan, a DBI graduate student in Electrical and Computer Engineering, used the SGI® OpenGL VolumizerTM API to write CAVEVOL, which enables scientists to display stereo models of microscopic cross-sections and other volumetric data in the Visualization Studio.
Under the advisement of Professor Gao, Thiagarajan also developed PATTVision, a visualization framework for discovering and comparing amino acid sequence patterns. "What PATTVision does, I believe for the first time, is take genomic analysis to the third dimension and allow us to detect Meta-Patterns for sequence homology analysis," says Thiagarajan. Using SGI Reality Center visualization power to travel along a molecule over a PATTVision buildup is like flying over a big-city skyline with color-coded buildings.
"Anti-aliasing is very important in this application," says Thiagarajan. "It really improves the clarity and definition of large-scale displays--a significant advantage of SGI hardware."
In the Institute's Bioimaging Center, scientists are using a multiphoton confocal microscope to capture images from a vascular corrosion cast of the kidney glomerulus (a capillary cluster that forms part of the kidney's blood-filtering system). The microscope produces 250-nanometer-thick optical slices to create a 3D image that can represent several millimeters of tissue depth.
"We started by microscopically imaging a half-inch-diameter rat kidney," Dr. Kirk Czymmek, director of the DBI Bioimaging Center, says. "In the studio, we then displayed a six-foot stereo version of the image that we can interactively manipulate and explore in three dimensions. Research is already underway to extend this approach to in vivo imaging of living cells and tissues in 3D and over time--an extremely powerful tool to better understand dynamic cellular processes."
The Future: Education and Haptic Interfaces
"When we configured the Visualization Studio, we wanted a tool that was both a research room and an education and training facility that seats 8 to 10 people comfortably," says Dr. Karl V. Steiner, DBI associate director. DBI is now working towards a program that will enable the institute to collaborate with hospitals on the use of its SGI visualization technology for training and education. DBI plans to develop and implement 3D visualization tools that display nondestructive imaging data from computer tomography, x-ray, ultrasound, and other sources for the training of interns.
Haptic feedback will be the next step in immersive visualization using SGI technology. A group in the University of Delaware's Department of Electrical and Computer Engineering, led by Professor Ken Barner, already uses two robot arms that are linked to the smaller SGI visualization facility. These robots provide tactile feedback based on interaction with virtual objects. "We are interested in taking this work further, developing algorithms that will simulate contact with soft tissue," says Barner. SGI technology will play a critical part in this.
SGI and DBI cosponsored a Life Sciences Summit on October 3, 2002, at the DBI facility in Newark, Delaware.
