VMD-L Mailing List

From: Robert Brunner (brunner_at_ks.uiuc.edu)
Date: Wed Jul 03 2002 - 16:19:02 CDT

JMV Molecular Viewer Support within BioCoRE

July 3, 2002:

Urbana, Illinois - The Theoretical Biophysics Group at the University of
Illinois is proud to announce an exciting new feature of BioCoRE, a
Biological Collaborative Research Environment. BioCoRE is freely
accessible at the Theoretical Biophysics Group website and development
is supported by the NIH National Center for Research Resources.

JMV <http://www.ks.uiuc.edu/Development/jmv/> version 1.0 can now be
accessed from within BioCoRE. JMV, a molecular viewer written using Java
and Java 3D, can be used to view molecular files stored within the
BioFS, BioCoRE's shared filesystem. JMV provides several molecular
representations, multiple coloring styles, lighting controls, and
stereoscopic rendering capabilities. Version 1.0 of JMV is currently
only available within BioCoRE, and a standalone release is upcoming.

In addition, several other BioCoRE components have seen key improvements
recently:

* The BioCoRE Control Panel can now be run as a standalone Java
application using Java Web Start. This frees users from the constraints
of running the Control Panel as a Java applet, which allows increased
flexibility and improved robustness since browser crashes no longer kill
the Control Panel.

* Improved overall "look and feel". The BioCoRE web pages no longer rely
on Javascript menus. This makes pages load faster and provides
compatibility with more browsers.

* Users can save JPEG files of states from VMD into BioCoRE
automatically. This allows researchers to browse states visually and
load desired configurations directly into VMD.

* You can now create Interactive accounts within Job Management.
Interactive accounts allow BioCoRE to submit jobs to any computer that
you can log into via SSH. This can be used to run jobs on machines that
BioCoRE doesn't officially support yet. (BioCoRE has built in support
for machines at PSC, NCSA and Globus sites using the Alliance
certificates)

* BioCoRE job management can now upload files to the remote
supercomputer center of your choice before submitting a job. This allows
researchers to keep their input files in the BioCoRE shared filesystem
and let BioCoRE automatically stage the files.

For details, please visit the BioCoRE website at
<http://www.ks.uiuc.edu/Research/biocore/>.

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!