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D. Osprey Change History

This appendix lists the changes from version to version in the Osprey distribution

Note that we tend to update the manual at the same time we make changes to Osprey, so the Manual is as dynamic as the application itself. Make sure that you are always using the latest Osprey manual to ensure that the procedures described are up to date.

- Changes made from Version 1.0.1 to Version 1.2.0

- WebStart capable for online viewing of interactions

- Support for Multiple Organisms such as Yeast, Fly, Human, Mouse, and most recently Worm (C.
  elegans), S. Pombe (Schizosaccharomyces pombe), Rat (Rattus norvegicus), and Zebra Fish (Danio rerio)

- Access to thousands of new interactions stored in The GRID (http://biodata.mshri.on.ca/grid/):
  -Yeast GRID contains 19039 unique interactions ( 14114 physical and 4925 genetic ).
  -Fly GRID contains 26596 unique interactions ( 20509 physical 6087 genetic ).
  -Worm GRID contains 4453 unique physical interactions.
- Increased memory to java vm in order to handle the large scale networks, see section 7.11 "Memory Setting" in the user manual on how to adjust the allocation of memory
- Improved functionality to organizing and adding new datasets, see section 3.1.4 "Opening Datasets" in the user manual
- Fixes to a number of small bugs found in 1.0.1.
- Updated User Manuals sections:

- 2.1.2 "Registering" minor update on how to register and download Osprey
- 2.5.3 "Running Osprey on Mac OS X ( versions 10.2 or Higher )" update to how Osprey is opened on the Mac OS X
- 2.7.3 "Uninstalling Osprey on Mac OS X ( versions 10.2 or Higher )" update to how Osprey is unistalled on the Mac OS X
- 3.1.4 "Opening Datasets" updated to indicated changes in the datasets available with Osprey and the ability to download new datasets
- 4.2.1 "File Menu" and 4.2.2 "Edit Menu" updated to show changes to both the datasets and the "change database" menu items
- 7.10 "Changing Database" section added to help explain the various databases Osprey can connect too
- 7.11 "Memory Setting" sections added to allow users to increase the amount of memory allocated to Osprey
- Appendix E "Purchasing Osprey Licenses for Commercial Organizations" added

- Changes made from Version 1.0.0 to Version 1.0.1

- Support for proxies and accessing The GRID through a web proxy

- Fix for a Mac font issue that prevents Osprey initialization in some cases on OS X

- Substantial speedup of Gene List and Custom Osprey file load times
- Automated detection of Osprey version upgrades, and new messaging system for informing Osprey users
- Fix for a bug in the latest Java update on the Mac that prevented Osprey from loading
- Moved the "Change Database" option to its own menu called "Database" for easier access

- Changes made from Version 0.9.10 to Version 1.0.0
  - Functional clustering added to the network layouts
  - Provide annotation for multiple organisms
  - Fully macOSX compatible
  - Greatly improved data retrieval speeds
  - A matrix output format for clustering
  - Graphics improvements
  - Several small bug fixes
  - Ability to add and search for multiple nodes
  - Ability to copy both node and edge annotation to the systems clip board for pasting into text editors
- Changes made from Version 0.9.9 to Version 0.9.10

- Fixed small problem with Edges not returning after a get all interactions call to the GRID
- Updated many links inside of the user manual that were non-existant or broken
- Fixed problem with Get All Interactions button on the Gene Info Display Area not properly enabling/disabling during normal operation

The Osprey Administrator
E-mail: ospreyadmin@mshri.on.ca

Copyright ©2002 Mount Sinai Hospital, Toronto, Ontario, Canada

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