BioCoRE release: New Features

Robert Brunner brunner at
Mon Dec 16 15:32:00 EST 2002

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. BioCoRE is available free 
of charge at

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 

     * 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

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 

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

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

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