JMV Molecular Viewer Support within BioCoRE

July 3, 2002 - 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 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

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

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