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BioCoRE - A Biological Collaborative
Research Environment

Urbana, Illinois - The Theoretical Biophysics Group at the University of Illinois is proud to announce the latest updates to the BioCoRE web-based collaborative research environment. Significant new features have been added, as well as many minor improvements and features suggested by our users. In addition, this release marks the first time that source code for the server is available. The BioCoRE server is available free of charge at http://www.ks.uiuc.edu/Research/biocore/localServer.

BioCoRE is a collaborative work environment for biomedical research, research management, and training. A resource-centered platform, BioCoRE offers scientists, working together or alone, a seamless interface to a broad range of local and remote technologies such as discipline-specific and general tools, and visualization solutions. In creating unprecedented proximity to colleagues' expertise and knowledge, BioCoRE empowers scientists everywhere, establishing equal access to research and training opportunities.

To harness and streamline collaborative capabilities across temporal and physical boundaries in research and training, BioCoRE builds on the transparent use of and communication between technological resources (hardware and software) and databases. BioCoRE features powerful yet easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and many others.

BioCoRE Features:

• Supercomputer Job Management: BioCoRE allows you to submit computational jobs to your supercomputer account at NCSA, PSC, and to other supercomputers using Globus via a web-based interface. After submitting jobs through BioCoRE, you may check back to see whether they have run, and view the output of the jobs as they run.
• Shared Molecular Visualization: Using the popular visual molecular dynamics program VMD (with support for the recently released version 1.8), BioCoRE users can share interesting views of molecules with collaborators around the world.
• Molecular Dynamics Simulation Config File Generator: BioCoRE includes a web-based graphical form that researchers can use to create input files for NAMD, a molecular dynamics simulation program that recently won the Gordon Bell award for high performance in parallel computing.
• Notebook: Researchers have access to online notebooks for archiving communication, keeping journals, and capturing output of computer programs. In addition, researchers can share lists of relevant websites with their collaborators.
• Shared filesystem: Scientists have access to a web-based shared filesystem that can be used to store important research files including documents being prepared for publication, PDF files, and more.
• Secure Instant Messaging: Via the BioCoRE "Control Panel" researchers can discuss their work in a secure environment. The Control Panel is also used to notify researchers of other important events, such as when new views are published from VMD, entries are added to the Notebook, and collaborators log in and out.
• and more!

In addition to accessing the above features at the online BioCoRE server in the Theoretical Biophysics Group, researchers can download and install their own BioCoRE server (available both in binary and source code form), for improved responsiveness and customizability.

For additional information, or to obtain a BioCoRE account, please visit the BioCoRE website at http://www.ks.uiuc.edu/Research/biocore/.

BioCoRE development is supported by the NIH National Center for Research Resources. The authors request that any published work which utilizes BioCoRE includes a reference to the BioCoRE webpage and/or the following reference:

BioCoRE: A collaboratory for structural biology. Milind Bhandarkar, Gila Budescu, William F. Humphrey, Jesus A. Izaguirre, Sergei Izrailev, Laxmikant V. Kale, Dorina Kosztin, Ferenc Molnar, James C. Phillips, and Klaus Schulten. In Agostino G. Bruzzone, Adelinde Uchrmacher, and Ernest H. Page, editors, Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, pages 242-251, San Francisco, California, 1999.

The Theoretical Biophysics group encourages BioCoRE users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to biocore@ks.uiuc.edu.

We are eager to hear from you, and thank you for using our software!