VMD-L Mailing List

From: Robert Brunner (brunner_at_ks.uiuc.edu)
Date: Fri Mar 03 2000 - 10:22:28 CST

This week we have released the initial version of our BioCoRe
collaborative research environment. Since interaction with VMD
will be a major component of the system, many of you may find it
useful. Details are included in the announcement below.

Robert Brunner
rbrunner_at_uiuc.edu

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Urbana, Illinois - The Theoretical Biophysics Group at the
University of Illinois is proud to announce the initial public release
of BioCoRE, a collaborative research environment. BioCoRE software is
freely available for use at the Theoretical Biophysics Group website.
BioCoRE development is supported by the NIH National Center for
Research Resources.

Modern computational structural biology requires scientists to employ a
wide range of tools and techniques to solve complex problems while
keeping accurate and complete records of research activities.
Additional complications are introduced by the need to effectively
engage in interdisciplinary collaborations with geographically
dispersed colleagues. The software BioCoRE, a collaborative research
environment for molecular modeling and simulations, addresses these
challenges.

Initial design work has led to a web-based architecture focused on four
primary interface paradigms:

  + a WORKBENCH interface includes features for controlling molecular
modeling, simulation, and bioinformatics tools with convenient and
uniform access to collaboratory data. Initial tools in this category
include the ability to start and monitor molecular dynamics simulations
via a web browser interface.

  + a NOTEBOOK interface automates recording of research activities.
Initial tools in this category include a notebook tool which can be used
by researchers to engage in offline discussions as well as review and
search the entire text of any prior chat session.

  + a CONFERENCE interface enables scientists to discuss their research
across distances in real time or time-delayed sessions and will spawn
software for teleconferencing and synchronized visualization of shared
data at distant sites. Initially, this category includes a text-based
chat mechanism where the researchers can choose topics and converse with
other researchers who are working on the same project.

  + a DOCUMENTS interface permits the preparation of multi-author
documents in a cross-platform revision control system.

BioCoRE consists of html and javascript and java where needed.

For additional information, please visit the BioCoRE website at
<http://www.ks.uiuc.edu/Research/collaboratory/>.

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 collaboratory_at_ks.uiuc.edu.

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