SCIENCE INDEX 2000 2001 2002 Physics

Web-based collaboration links labs to supercomputers

Jim Barlow, Life Sciences Editor
(217) 333-5802; b-james3@uiuc.edu

9/3/02

CHAMPAIGN, Ill. — Researchers collaborating by means of the Internet is nothing new. However, an evolving Web-based environment created at the University of Illinois at Urbana-Champaign is redefining long-range collaboration and linking far-away labs to supercomputers – for free.

Currently more than 500 researchers are involved in more than 100 projects using the Biological Collaborative Research Environment for Structural Biology, or BioCoRE.

Created initially with biomedical research in mind, BioCoRE is being made available to scientists in any research and training area. It was developed by the Theoretical Biophysics Group at the Beckman Institute for Advanced Science and Technology.

"This is a visionary program," said Klaus Schulten, holder of the Swanlund Chair in Physics and the Theoretical Biophysics Group director. "BioCoRE is a virtual science laboratory and classroom. We have developed an America Online for biomedical researchers and trainees, and now it can serve scientists in many other fields. It lets researchers do experiments and teach as if they are all in a single room, but they can be anywhere."

BioCoRE is under continuing development with funding from the National Institutes of Health. Lead researchers are Schulten; Gila Budescu, a social scientist; and computer scientist Laxmikant V. Kale.

"When we started, we designed BioCoRE to emulate our facility at the Beckman Institute, where individuals from different fields work together; they have their own offices and access to public places and use the resources for cross-disciplinary collaboration," said Budescu, who oversees the development area. "The BioCoRE virtual environment, with its shared project spaces, bridges disciplinary, temporal and geographical boundaries and offers an optimal and powerful extension to a normal physical office and classroom."

BiCoRE members can readily access – regardless of their computer operating systems – computational tools, data record-keeping capabilities, communications and document storage, all of which harness the entire research and training process. With BioCoRE, users with supercomputer accounts gain seamless access to major National Science Foundation centers, such as NCSA at Illinois and PSC at Pittsburgh.

Scientists communicate by way of a control panel, similar to instant-messaging software, and can access a complete archive to review discussions they may have missed. Thus, team members in different locations can carry on conversations, participate in workshops, and share ideas interactively, said Robert Brunner, a BioCoRE developer who is completing his doctorate in electrical engineering.

"There is no lag time to slow down creativity," he said. By accessing a protein databank, for example, collaborators can jointly manipulate 3-D models of selected proteins. Using JMV, a newly developed Java Molecular Viewer program, each new view can be immediately saved and placed back on the server, Brunner said. Other team members can then quickly view the images – even those members who don’t have JMV installed on their computers.

BioCoRE is organized around projects and/or training topics, and for security, confidentiality and privacy reasons BioCoRE members can only see their own projects, said developer Kirby Vandivort, a computer scientist and nuclear engineer. "If you are not in a particular project, you don’t know it exists."

BioCoRE has advanced dramatically since its initial release in March 2000. Earlier this year, the BioCoRE server software became available for download, allowing scientists to set up their own personal servers. BioCoRE supports in-house and third-party tools. The Theoretical Biophysics Group’s other major software products – the visualization program VMD and the molecular dynamics simulation program NAMD – are easily launched from within BioCoRE. More information is available on the Web at http://www.ks.uiuc.edu/Research/biocore and http://www.ks.uiuc.edu.