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1. General Information

The Osprey Network Visualization System (Copyright ©2002 Mount Sinai Hospital) is a tool for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale data sets can be readily combined with Osprey for comparison of different methods. The Osprey Network Visualization System is a copyright of the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto, Ontario, Canada.

For all of the latest information about Osprey, including latest patches and updates, please visit the Osprey web site ( http://biodata.mshri.on.ca/osprey ).

The following list describes some sections of particular interest in this manual:

- For information about the developers and team behind Osprey, see appendix B. Credits
- For information about joining the Osprey mailing list, see section 1.6 Joining the Osprey Mailing List
- For installation instructions, see section 2. Osprey Installation
- For a listing of basic Osprey layouts and descriptions, see section 4. Basic Introduction
- For a history of new features and bug fixes, see appendix D. Osprey Change History
- For a list of currently known bugs and misfeatures, see appendix A. Known Problems and Common Errors
- For future Osprey plans, see appendix C. Future Updates and Obtaining Patches
- For more information about The GRID, see section 8. The GRID ( The General Repository of Interaction Datasets )

## Important:

Reports of any errors ( often called bugs ), as well as questions and comments, should be sent to ospreyadmin@mshri.on.ca . For more information on contacting us, please see section 1.4 Contact Information

1.1 About this Manual

This is the Osprey Network Visualization System manual. Being a reference manual, it does not provide any general information on the actual development involved in the product. No documentation of source code or tools is provided within.

As Osprey is under constant development, this manual is also updated frequently. The most recent version of the manual is available at ( http://biodata.mshri.on.ca/osprey ) in various formats.

If you have any suggestions concerning additions or corrections to this manual, please send them to the documentation team at ospreyadmin@mshri.on.ca .

This manual was initially written by Bobby-Joe Breitkreutz, Chris Stark, and Hosam Abdulrrazek. It is currently maintained by the Osprey development team at Mount Sinai Hospital. For other contributors, please see section B. Credits,

The copyright ( © 2002 ) to this manual is owned by Mount Sinai Hospital in Toronto, Ontario. See section 1.3 Copyright Notice .

This manual is best viewed with Microsoft Internet Explorer version 6.0+ or Netscape/Mozilla version 1.1+

1.1.1 Conventions used in this manual

This manual uses the following Typographical Conventions:

Links

> > Represents Links either to external pages, or to other pages inside this reference manual

HEADINGS

> > Denotes the start of a new section or subsection in this manual

1.2 What is Osprey

Osprey is a tool for graphically representing biological interactions. It can be used in one of two ways:

1. As a freely distributed standalone version available at ( http://biodata.mshri.on.ca/osprey )
2. As an add-on interaction visualization system for use with online interaction databases (see section 1.5 Osprey Licensing for more details)

For all of the latest information concerning Osprey, please visit the Osprey web page at ( http://biodata.mshri.on.ca/osprey )

1.2.1 The Main Features of Osprey

The following list describes some of the important characteristics of the Osprey Network Visualization System:

- Portability ( cross platform availability )
  - Osprey is available on almost all Platforms that support the latest Java Plugin
- Tools for Biological Analysis
  - Osprey provides many features such as network filters, connectivity filters, advanced layouts, and dataset superimposing which are extremely useful to biologists who are interested in analyzing their data
- Powerful Support Database
  - Integrated with Osprey is a powerful database of interactions and annotation, see section 8. The GRID ( The General Repository of Interaction Datasets ).
- Ease of use
  - Osprey provides an extremely user friendly interface for working with interaction data
- Online Database Add-on Ability
  - Osprey can be incorporated as a standard visualization tool with online databases such as The GRID ( http://biodata.mshri.on.ca/grid )
- Support for figures
  - Osprey networks can be saved in SVG, PNG and JPG format so they can be used with image programs

1.3 Copyright Notice

Copyright ©2002 Mount Sinai Hospital, Toronto, Canada. All Rights Reserved.

Warning: This system may be monitored by system or security personnel.

License Agreement for the Osprey Network Visualization System and all documentation

THIS AGREEMENT SETS OUT THE TERMS AND CONDITIONS FOR DOWNLOADING, COPYING, INSTALLING, OR USING OSPREY NETWORK VISUALIZATION SYSTEM SOFTWARE AND ASSOCIATED MATERIAL AND DOCUMENTATION INCLUDING ANY MODIFIED VERSIONS OR UPDATES (COLLECTIVELY “SOFTWARE”).

READ THE TERMS OF THIS AGREEMENT AND ANY PROVIDED SUPPLEMENTAL LICENSE TERMS (COLLECTIVELY "AGREEMENT") CAREFULLY BEFORE OPENING THE SOFTWARE PACKAGE. BY OPENING THE SOFTWARE PACKAGE, YOU AGREE TO THE TERMS OF THIS AGREEMENT AND THAT IT IS ENFORCEABLE LIKE ANY WRITTEN NEGOTIATED AGREEMENT SIGNED BY YOU. INDICATE YOUR ACCEPTANCE OF THESE TERMS BY SELECTING THE "ACCEPT" BUTTON AT THE END OF THIS AGREEMENT. IF YOU DO NOT AGREE TO ALL OF THESE TERMS, SELECT THE "DISAGREE" BUTTON AT THE END OF THIS AGREEMENT AND THE SOFTWARE DOWNLOAD WILL NOT CONTINUE.

Restrictions

All downloads and use of the Osprey Network Visualization System are subject to the following terms:

As long as you comply with the terms of this Agreement, you are granted a non-exclusive license to install and use the Software on a single computer for educational, research, and not-for-profit purposes, without fee. Except as expressly permitted in this Agreement, you may not use, copy, decompile, reverse engineer, disassemble, modify, rent, lease, loan, sublicense, distribute or create derivative works based upon the Software in whole or part or transmit the Software over a network.

You shall not remove any copyright notices or other proprietary notices from the Software.

Except as expressly stated herein this Agreement does not grant you any intellectual property rights in the Software and all rights not expressly granted herein are reserved by Mount Sinai Hospital.

The right to download, copy, install, use, and distribute this software and its documentation by companies or other for profit organizations or in conjunction with for profit activities, are not granted except by prior written arrangement of the copyright holder. For commercial licensing opportunities contact ospreyadmin@mshri.on.ca or visit http://biodata.mshri.on.ca/osprey/servlet/CommercialRegistration/ for more details.

Termination

This Agreement and your license to use the Software will continue so long as you remain in compliance with the terms and conditions of this Agreement. Your license will terminate automatically without notice from Mount Sinai Hospital if you breach any of your obligations hereunder. Upon termination, you shall cease using the Software and shall destroy all copies of the Software (and associated materials and documentation) in any form. All disclaimers of warranties and limitations of liability shall survive any termination of this Agreement.

Disclaimers

IN NO EVENT SHALL MOUNT SINAI HOSPITAL BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OR INABILITY TO USE THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF MOUNT SINAI HOSPITAL HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

THE SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". MOUNT SINAI HOSPITAL SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OF ANY KIND INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY, NONFRINGEMENT, AND FITNESS FOR A PARTICULAR PURPOSE. MOUNT SINAI HOSPITAL HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. MOUNT SINAI HOSPITAL DOES NOT WARRANT OR ASSUME RESPONSIBILITY FOR THE ACCURACY OR COMPLETENESS OF ANY INFORMATION, TEXT, GRAPHICS, LINKS, OR OTHER ITEMS CONTAINED WITHIN THE SOFTWARE.

Published research assisted by this software should cite:

Breitkreutz, BJ., Stark, C., Tyers M. "Osprey: A Network Visualization System." Genome Biology 2003 4(3):R22

1.4 Contact Information

For commercial licensing opportunities, suggestions, corrections, bug reports, more information or for joining our mailing list, contact::

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

1.5 Osprey Licensing

Please see section E. Purchasing Osprey Licenses for Commercial Organizations for full details of Osprey licensing policy.

1.6 Joining the Osprey Mailing List

To be kept up to date on all the latest bug fixes, version releases, and other information about the Osprey Network Visualization System, please subscribe to the Osprey mailing list by sending an email to:

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

Or visit the Osprey web site at http://biodata.mshri.on.ca/Osprey

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