New Features Added to This Version

The new Beta Release includes a subset of VBI tools that have been tested recently. New features and bug fixes have been made to ToolBus, web services and visualization plugins. Performance and usability have been improved for this release. A new microarray plugin is under development, so microarray plugin is not included in this release.

New Features:

• The new release supports new web service input form. The form now has a brand new look, it groups related parameters together. The grouped parameters can collapse or expand by clicking a button. Some related operations are also merged together, for example, the blastn_Basic, blastn_Advanced have been merged into a single blastn operation. The web services affected by this change are: MUMmer, Glimmer, ProbeDesign, ClusterBlast, Stretcher, Water, ClustalW.
• The performance of some web services has been tuned, MUMmer and GenomeTool should work faster than previous version.
• Memory usage has been optimized. The new release of ToolBus will use less memory than previous versions and can handle larger datasets.
• A Bug Report menu item has been added to the ToolBus Help menu. Users can suggest new features or report bugs using this menu.
• ToolBus tutorial and FAQ have been updated to reflect the most recent changes in ToolBus.
• Model Tool Editor is changed. The new Reset button will load model tools originally defined in the plugin package. After a plugin is loaded into memory, it will look for user saved model tools to overwrite the model tools defined in the plugin. Clicking the Reset button will reverse this change.
• The "Show this window for single model" option checkbox is added to model chooser. Unchecking this option will not show model chooser when a web service returns with only a single model discovered. This option can be checked back from the preference editor window.
• Following bug fixes have been fixed since last beta release(27FEB2006):
  Add YODA tool and fix a bug for MAC. Fix bugs for probe design plugin.
  Set plain text file as the default export file type, if user does not give file extension, it will append .txt to the file.
  Temporarily remove parallel view from mummer plugin.
  Remove BioPAX support from ProNet plugin for using pronet on Mac.
  Remove user login window and data uploading from DASView.
  Show cursor in blink mode for text finding function.
  Change Font Color menu to Block Color menu to avoid misunderstanding in sequence alignment viewer.
  Remove Search tab from AddTools panel temporarily, IBM no longer supports for UDDI Registry.
  
• New bug fixes and improvements to gencomp(mummer) and dasview viewer(12June2006).
  DTD upgrade for ProNet.
  Bug fix in Dasview for missing contigs(11July2006).
  Updates and bug fixes on Phylogenetic viewer, removing table view and supporting failover(10Aug2006).
  Bug fix to ToolBus to catch an exception which may hang up ToolBus during startup (25Aug2006).
  Updating on Phylogenetic Tree plugin, ToolBus tutorial and session file(11SEP2006).
  Session file is updated, which replaces www.vbi.vt.edu with pathport.vbi.vt.edu(5APR2007).
  
• The installation process has been simplified. Now only one step is required to download ToolBus and Plugins.

Limitations:

• This release preconfigured only a subset of web services that have been fully tested internally. We have developed a wide variety of web services, they can be added to ToolBus easily. We will continue to increase this subset as enhancements and testing are completed.