VMD-L Mailing List

From: Robert Brunner (brunner_at_ks.uiuc.edu)
Date: Mon Dec 16 2002 - 17:04:02 CST

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_at_ks.uiuc.edu.

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