Press Archive

SDSC to Debut "Cool" New Collaboration Environment at Supercomputing '96

Published 11/13/1996

For more information, contact:
Ann Redelfs, SDSC
619-534-5032/5113 (fax)

San Diego, CA -- At Supercomputing '96 (November 17-21) in Pittsburgh, SDSC researchers will demonstrate publicly for the first time a new Immersive Collaborative Environment (ICE) with a specific application in protein structure analysis. By integrating innovative visualization technologies with biological databases and software, SDSC's Molecular ICE project opens up new worlds of interaction and cooperation for scientists.

ICE implements a vision of how scientists will take advantage of the next-generation Internet for scientific applications by harnessing technologies at the cutting edge of supercomputing, virtual reality, and rapid prototyping. In particular, the Molecular ICE project explores how immersive technology can benefit molecular modeling, improves methods for interactive visualizations of molecular structures, and lets remote researchers work together on the same molecular model.

Biologists need to understand how proteins work in order to design drugs that bind to them and change their activity, perhaps by interfering with a malfunctioning neurotransmitter or latching onto a toxin molecule before it does damage. Key to this understanding is the 3-D structure of the protein, DNA, or other biological macromolecule. Seeing the complex folding patterns and detailed interactions between atoms reveals how and why a protein acts as it does.

"The amino acids determine the structure of a protein and what that protein does in the body," said Michael Gribskov. "But we're just starting to get a handle on how they do this." Gribskov is leading efforts at SDSC to map sequence data onto 3-D structure, a key component of Molecular ICE, which will allow biologists to examine the twists and turns of protein structures almost as if they were inside the molecule.

A joint effort between researchers from SDSC's Computational Biology group and Advanced Scientific Visualization Laboratory (VisLab), the Molecular ICE project stands to benefit not only biologists, but also scientists from many other disciplines. With appropriate extensions, the same environment could be applied by scientists to debate the evolutionary history of species in 3-D phylogenetic trees, to explore geologic landscapes models, or to design complex mechanical parts.

The Molecular ICE project combines SDSC's expertise in visualization technologies and biology databases and software to provide a tool that spans the computational science process--from computing data to visualizing and analyzing the results to producing output.

To search for proteins that contain relevant sequences from databases of thousands of proteins, biologists can take advantage of "transparent supercomputing" applications at SDSC that have been integrated into ICE. One in particular, MEME, was developed by Timothy Bailey, Charles Elkan, and Bill Grundy of UCSD's Computer Science and Engineering department to search for common protein subsequences using techniques ranging from simple text searches to complex pattern matching. MEME is one of the computational tools provided to the biomedical community by the National Biomedical Computation Resource project, on which Gribskov is a principal investigator and which joins researchers at SDSC, UC San Diego, Biosym Technologies, The Scripps Research Institute, and UC San Francisco.

Implemented on SDSC's Intel Paragon and CRAY T3D, MEME allows users to conduct computationally intensive protein sequence searches through a Web interface. The system "transparently" makes supercomputer power available without requiring biologists to delve into the complexities of parallel programming. MEME returns matching sequences, from which a biologist can isolate a particular sequence for visualization.

ICE software translates the sequence into a Virtual Reality Modeling Language (VRML) model annotated with sequence information. With the VRML molecule, collaborating researchers at remote locations then can explore the structure jointly. Standard VRML browsing gives each viewer a separate copy of the 3-D world, but ICE allows researchers to interact simultaneously with the same VRML molecular "world." When one researcher manipulates the molecule, by zooming, rotating, or panning, remote collaborators see the same movement.

"The collaborative capabilities were added into SDSC's VRBS [Virtual Reality Behavior System] engine with which WebView communicates," said SDSC programmer/analyst John Moreland. "A VRBS server was also developed that ties ICE client applications together."

ICE also extends WebView, SDSC's own VRML browser, to let a user in SDSC's VisLab navigate a VRML world using a FakeSpace Boom. The Boom not only provides a stereoscopic interface for any VRML world, but also allows the user to move around in the VRML world by moving bodily in the real world. ICE will eventually allow the user to trigger actions with a hand-held wand developed by Moreland and containing a Polhemus 3-D tracking system that provides position and orientation information.

"One of our highest priority goals is to migrate the ICE environment to VRML 2.0 for its content description and its 3D interaction," said Allan Snavely, head of SDSC's interaction environments group. "We plan to enable the ICE environment to run under any VRML 2.0-compliant browser or plug-in and to extend and improve its tightly coupled 2-D Web interface."

To produce 3-D output that complements the 3-D worlds, ICE provides a user with the option of "printing" a solid model of a molecule on SDSC's TeleManufacturing Facility (TMF). The TMF, centered around a Laminated Object Manufacturing device in SDSC's VisLab, lets researchers across the Internet produce solid models from 3-D geometry sets. In ICE, a user can request to send a molecular model to the TMF through the WebView browser.

"In fact, ICE contains no code that is specific to any one type of scientific content," Snavely said. "If you want discipline-specific features in an ICE application, you could easily add them. If you can author it, ICE will support it."

SDSC, a national laboratory for computational science and engineering, is sponsored by NSF, other federal agencies, the State and University of California, and private organizations; is affiliated with the University of California, San Diego; and is administered by General Atomics. For more information, see or contact Ann Redelfs, SDSC,, 619-534-5032.