Osprey Network Visualization System

Reference Manual for Version 1.2.0

1. General Information
  1.1 About this Manual
    1.1.1 Conventions Used in the Manual
  1.2 What is Osprey?
    1.2.1 The Main Features of Osprey
  1.3 Copyright Notice
  1.4 Contact Information
  1.5 Osprey Licensing
  1.6 Joining the Osprey Mailing List
2. Osprey Installation
  2.1 Obtaining Osprey
    2.1.1 The Osprey Homepage
    2.1.2 Registering
    2.1.3 Downloading
      2.1.3.1 Downloading for Windows
      2.1.3.2 Downloading for Red Hat
      2.1.3.3 Downloading for Mac OS X
  2.2 Standard Installation Procedure for Microsoft Windows Systems ( ME, XP, 2000, 98, 95, NT )
  2.3 Standard Installation Procedure for Red Hat Linux Systems ( versions 7.3 or Higher )
  2.4 Standard Installation Procedure for Mac OS X ( versions 10.2 or Higher )
  2.5 Post Installation
    2.5.1 Running Osprey on Microsoft Windows Systems ( ME, XP, 2000, 98, 95, NT )
    2.5.2 Running Osprey on Red Hat Linux Systems ( versions 7.3 or Higher )
    2.5.3 Running Osprey on Mac OS X ( versions 10.2 or Higher )
  2.6 Common Installation Issues
  2.7 Uninstalling Osprey
    2.7.1 Uninstalling Osprey on Microsoft Windows Systems ( ME, XP, 2000, 98, 95, NT )
    2.7.2 UninstallingOsprey on Red Hat Linux Systems ( versions 7.3 or Higher )
    2.7.3 Uninstalling Osprey on Mac OS X ( versions 10.2 or Higher )
  2.8 Version Checking
3. Opening and Saving Files
  3.1 Types of Files Opened by Osprey
    3.1.1 Osprey File
    3.1.2 Custom File
      3.1.2.1 Custom File Variation #1
      3.1.2.2 Custom File Variation #2
      3.1.2.3 Custom File Variation #3
      3.1.2.4 Custom File Variation #4
    3.1.3 Gene List
      3.1.3.1 Gene List Variation #1
      3.1.3.2 Gene List Variation #2
    3.1.4 Opening Datasets
      3.1.4.1 Downloading new datasets
      3.1.4.2 Adding personal datasets
    3.1.5 Superimposing Datasets
  3.2 Saving to Osprey Files ( .osp )
  3.3 Exporting
    3.3.1 Image Types
      3.3.1.1 JPEG
      3.3.1.2 PNG
      3.3.1.3 SVG (Scalable Vector Graphics)
    3.3.2 Matrix
    3.3.3 How to Export
4. Basic Introduction
  4.1 Osprey Layout
  4.2 Osprey Menus
    4.2.1 File Menu
    4.2.2 Edit Menu
    4.2.3 View Menu
    4.2.4 Insert Menu
    4.2.5 Format Menu
    4.2.6 Filter Menu
    4.2.7 Layout Menu
    4.2.8 Help Menu
    4.2.9 Database Menu
  4.3 Networks
    4.3.1 Network Display Area
    4.3.2 Manipulating the Network
      4.3.2.1 Selecting Nodes
      4.3.2.2 Selecting Edges
      4.3.2.3 Moving Individual Nodes
      4.3.2.4 Selecting Multiple Nodes
      4.3.2.5 Moving Multiple Nodes
      4.3.2.6 Removing Nodes
      4.3.2.7 Removing Edges
      4.3.2.8 Showing Loner Nodes
    4.3.3 Network Display Area Command Menu
  4.4 Gene/Edge Info Area
   

4.4.1 Changing Screen Name

    4.4.2 Adding Comments
    4.4.3 Viewing Selected Node Report
    4.4.4 Update Annotation
    4.4.5 Edge Info
  4.5 Adding Interactions
    4.5.1 From the Orf Info Area
    4.5.2 From the Network Display Area Command Menu and Insert Menu
      4.5.2.1 Adding all interactions to selected vertices
      4.5.2.2 Adding only interactions within Selected Vertices
  4.6 Colour Indices
    4.6.1 Go Process Index
    4.6.2 Experimental Systems Index
    4.6.3 Sources Index
    4.6.4 Saving Colour Indices
  4.7 Multiple Organism Support
5. Filters
  5.1 Network Filters
    5.1.1 Accessing Network Filters
    5.1.2 Using the Network filtering windows
      5.1.2.1 Overview of the network filtering window
      5.1.2.2 Filtering nodes out
      5.1.2.3 Adding nodes back
      5.1.2.4 Grouping items
    5.1.3 Experimental Systems
    5.1.4 Sources
    5.1.5 GO Process
    5.1.6 Turn Off Filters
  5.2 Connectivity Filters
    5.2.1 Accessing Connection Filters
    5.2.2 Minimum
    5.2.3 Iterative Minimum
    5.2.4 Depth
    5.2.5 Turn Off Connectivity
6. Layouts
  6.1 Auto Relaxation
    6.1.1 Accessing the auto relaxation from the main menu
  6.2 Circular Layouts
    6.2.1 One Circle
      6.2.1.1 Accessing the one circle layout
    6.2.2 Concentric Circles
      6.2.2.1 Accessing the concentric circles layout
    6.2.3 Concentric Circles Options
      6.2.3.1 Accessing the Concentric Circles Options
  6.3 Dual Ring Layouts
  6.4 Spokes
    6.4.1 Default Spokes
      6.4.1.1 Accessing the default spoke model
    6.4.2 Forced Spokes
      6.4.2.1 Accessing the forced spoke model
    6.4.3 Spoke Options
      6.4.3.1 Accessing the spoke options
  6.5 Global Layouts
    6.5.1 Spoked Dual Ring
      6.5.1.1Accessing Spoked Dual Ring Layout
    6.5.2 Spoked Dual Ring Options
      6.5.2.1 Accessing Spoked Dual Ring Layout Option settings
  6.6 Functional Clustering
    6.6.1 Accessing Functional Clustering options
    6.6.2 GO Proccess Order
    6.6.3 Cluster Gap Size
   

6.6.4 Turning Functional Clustering On/Off

   

6.6.5 Degree of GO Process colouring

7. Osprey Preferences and Customization
  7.1 Graph Colouring
    7.1.1 Accessing Graph Colouring
  7.2 Drawing / Dragging Graph options
    7.2.1 Accessing Drawing/Dragging graph options
  7.3 Node Options
    7.3.1 Choosing Method of Colouring Nodes
    7.3.2 User Defined Node Colours
    7.3.3 Colour Choosing Window
      7.3.3.1 Swatches tab
      7.3.3.2 HSB tab
      7.3.3.3 RGB tab
    7.3.4 Node Size
  7.4 Edge Options
    7.4.1 Choosing Method of Colouring Edges
    7.4.2 User Defined Edge Colours
    7.4.3 Edge Size
  7.5 Arrow Head Options
    7.5.1 User Defined Arrow Head Colour
    7.5.2 Arrow Head Size
  7.6 Label Options
    7.6.1 Label Size
    7.6.2 Label Font
    7.6.3 Label Style
    7.6.4 Label Colour
    7.6.5 Hiding Labels
  7.7 Background Colour
    7.7.1 Accessing Background Colour
  7.8 Saving Preferences
    7.8.1 Saving settings
      7.8.1.1 Saving Advanced Settings
      7.8.1.2 Saving Colour Settings
  7.9 Proxy Settings
  7.10 Changing Databases
  7.11 Memory Settings
8. The GRID ( The General Repository of Interaction Datasets )
  8.1 Where to find The GRID
  8.2 Osprey and The GRID
A. Known Problems and Common Errors
  A.1 What to do if you Encounter an Error
  A.2 The Osprey Error Log
  A.3 Reporting Errors to the Osprey Team
  A.4 Known Problems
  A.5 Common Errors
    A.5.1 Unable to Install Osprey under a Windows 2000, NT, or XP
    A.5.2 Unable to Add Interactions
B. Credits
  B.1 The Osprey Team
  B.2 The Osprey Contributors
  B.3 The Osprey Supporters
C. Future Updates and Obtaining Patches
D. Osprey Change History
E. Purchasing Osprey Licenses for Commercial Organizations
  E.1 Commercial Applications