NCSA NEWS

Biological researchers across the country and around the globe can easily collaborate with peers and seamlessly manage computational resources thanks to an online environment now available through NCSA.

BioCoRE (Biological Collaborative Research Environment) is a web-based collaborative laboratory, or "collaboratory." It is a portal to a suite of tools to help scientists discuss projects, submit and track jobs running on various high-performance computers, share molecular visualizations and other data, collaborate on experiments, and exchange and share files.

"BioCoRE is a virtual science laboratory and classroom," explained Klaus Schulten, a physics professor and the leader of the Theoretical and Computational Biophysics Group at the University of Illinois' Beckman Institute. The BioCoRE project was launched under his direction about three and a half years ago with funding from the National Institutes of Health. "It lets researchers do experiments and teach as if they are all in a single room, but they can be anywhere."

And BioCoRE's users are everywhere. There are more than 700 registered users worldwide; more than 50 percent are in the United States, but others come from the United Kingdom, Japan, India, France, Egypt, Malaysia, and 39 other countries around the globe.

BioCoRE's features include:

• A Job Manager that allows scientists to submit jobs to National Science Foundation high-performance computers, including those at NCSA. Users can also use BioCoRE to input their data and receive results. With BioCoRE, users can begin viewing the output of their computations while the job is still running, which can lead to early detection of flawed input and can save precious machine hours.
• An interface to NAMD, a code that simulates the atom-by-atom behavior of large biomolecules and bimolecular systems. BioCoRE makes it much easier to create and edit NAMD input files.
• Tools to save and share the 3D molecular visualizations created in VMD.
• An easy-to-use shared file system. Shared files are represented by the same type of icons as files and programs that live on a user's desktop computer, so opening a shared file is as simple and intuitive as double-clicking.
• A message board and online lab notebook to help distant collaborators communicate and stay in sync.

"We have tried to include the complete process, from when you're talking to your collaborators about what you plan to do, to conducting the research, managing supercomputing jobs, and then writing up the results for publication," said Kirby Vandivort, a senior research programmer with Schulten's group.

NCSA now has an in-house BioCoRE server. "This is a good example of the type of environment that simplifies access to the Grid," said NCSA senior research programmer Rick Kufrin.

The BioCoRE team will demonstrate the system at the NCSA booth at SC2003, to be held in Phoenix, Arizona, Nov. 15-21.

For more information on BioCoRE, go to http://biocore.ncsa.uiuc.edu/ and http://www.ks.uiuc.edu/Research/biocore/.

Access Online | Posted 9-9-2003