| 1. General
Information |
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1.1 About this Manual |
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1.1.1 Conventions Used in the Manual |
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1.2 What is Osprey? |
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1.2.1 The Main Features of Osprey |
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1.3 Copyright Notice |
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1.4 Contact Information |
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1.5 Osprey Licensing |
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1.6 Joining the Osprey Mailing List |
| 2. Osprey Installation |
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2.1
Obtaining Osprey |
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2.1.1
The Osprey Homepage |
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2.1.2
Registering |
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2.1.3
Downloading |
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2.1.3.1 Downloading for Windows |
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2.1.3.2
Downloading for Red Hat |
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2.1.3.3
Downloading for Mac OS X |
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2.2
Standard Installation Procedure for Microsoft Windows Systems (
ME, XP, 2000, 98, 95, NT ) |
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2.3
Standard Installation Procedure for Red Hat Linux Systems (
versions 7.3 or Higher ) |
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2.4
Standard Installation Procedure for Mac OS X ( versions 10.2 or
Higher ) |
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2.5 Post
Installation |
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2.5.1 Running Osprey on Microsoft Windows Systems ( ME,
XP, 2000, 98, 95, NT ) |
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2.5.2 Running Osprey on Red Hat Linux Systems (
versions 7.3 or Higher ) |
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2.5.3 Running Osprey on Mac OS X ( versions 10.2 or
Higher ) |
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2.6
Common Installation Issues |
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2.7
Uninstalling Osprey |
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2.7.1 Uninstalling Osprey on Microsoft Windows Systems
( ME, XP, 2000, 98, 95, NT ) |
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2.7.2 UninstallingOsprey on Red Hat Linux Systems (
versions 7.3 or Higher ) |
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2.7.3 Uninstalling Osprey on Mac OS X ( versions 10.2
or Higher ) |
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2.8
Version Checking |
| 3.
Opening and Saving Files |
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3.1 Types of Files
Opened by Osprey |
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3.1.1
Osprey File |
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3.1.2
Custom File |
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3.1.2.1
Custom File Variation #1 |
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3.1.2.2
Custom File Variation #2 |
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3.1.2.3
Custom File Variation #3 |
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3.1.2.4
Custom File Variation #4 |
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3.1.3
Gene List |
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3.1.3.1
Gene List Variation #1 |
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3.1.3.2
Gene List Variation #2 |
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3.1.4
Opening Datasets |
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3.1.4.1
Downloading new datasets |
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3.1.4.2
Adding personal datasets |
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3.1.5
Superimposing Datasets |
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3.2 Saving to Osprey
Files ( .osp ) |
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3.3 Exporting |
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3.3.1
Image Types |
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3.3.1.1
JPEG |
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3.3.1.2
PNG |
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3.3.1.3
SVG (Scalable Vector Graphics) |
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3.3.2
Matrix |
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3.3.3
How to Export |
| 4. Basic Introduction |
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4.1 Osprey Layout |
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4.2 Osprey Menus |
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4.2.1 File Menu |
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4.2.2 Edit Menu |
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4.2.3 View Menu |
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4.2.4 Insert
Menu |
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4.2.5 Format
Menu |
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4.2.6 Filter
Menu |
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4.2.7 Layout
Menu |
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4.2.8 Help Menu |
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4.2.9 Database
Menu |
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4.3 Networks |
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4.3.1 Network
Display Area |
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4.3.2
Manipulating the Network |
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4.3.2.1
Selecting Nodes |
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4.3.2.2
Selecting Edges |
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4.3.2.3 Moving
Individual Nodes |
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4.3.2.4
Selecting Multiple Nodes |
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4.3.2.5 Moving
Multiple Nodes |
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4.3.2.6
Removing Nodes |
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4.3.2.7
Removing Edges |
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4.3.2.8
Showing Loner Nodes |
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4.3.3 Network
Display Area Command Menu |
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4.4 Gene/Edge
Info Area |
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4.4.1 Changing Screen
Name
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4.4.2 Adding
Comments |
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4.4.3 Viewing
Selected Node Report |
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4.4.4 Update
Annotation |
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4.4.5 Edge Info |
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4.5 Adding
Interactions |
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4.5.1 From the
Orf Info Area |
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4.5.2 From the Network Display Area Command Menu and Insert Menu |
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4.5.2.1 Adding
all interactions to selected vertices |
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4.5.2.2 Adding
only interactions within Selected Vertices |
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4.6 Colour
Indices |
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4.6.1 Go
Process Index |
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4.6.2
Experimental Systems Index |
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4.6.3 Sources
Index |
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4.6.4 Saving
Colour Indices |
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4.7 Multiple
Organism Support |
| 5. Filters |
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5.1 Network Filters |
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5.1.1 Accessing
Network Filters |
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5.1.2 Using the
Network filtering windows |
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5.1.2.1 Overview
of the network filtering window |
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5.1.2.2 Filtering
nodes out |
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5.1.2.3 Adding
nodes back |
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5.1.2.4 Grouping
items |
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5.1.3 Experimental
Systems |
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5.1.4 Sources |
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5.1.5 GO Process |
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5.1.6 Turn Off
Filters |
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5.2 Connectivity
Filters |
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5.2.1 Accessing
Connection Filters |
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5.2.2 Minimum |
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5.2.3 Iterative
Minimum |
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5.2.4 Depth |
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5.2.5 Turn Off
Connectivity |
| 6. Layouts |
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6.1 Auto Relaxation |
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6.1.1 Accessing the
auto relaxation from the main menu |
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6.2 Circular Layouts |
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6.2.1 One Circle |
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6.2.1.1 Accessing
the one circle layout |
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6.2.2 Concentric
Circles |
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6.2.2.1 Accessing
the concentric circles layout |
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6.2.3 Concentric
Circles Options |
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6.2.3.1 Accessing
the Concentric Circles Options |
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6.3 Dual Ring
Layouts |
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6.4 Spokes |
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6.4.1 Default
Spokes |
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6.4.1.1 Accessing
the default spoke model |
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6.4.2 Forced
Spokes |
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6.4.2.1 Accessing
the forced spoke model |
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6.4.3 Spoke
Options |
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6.4.3.1 Accessing
the spoke options |
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6.5 Global Layouts |
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6.5.1 Spoked Dual
Ring |
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6.5.1.1Accessing
Spoked Dual Ring Layout |
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6.5.2 Spoked Dual
Ring Options |
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6.5.2.1 Accessing
Spoked Dual Ring Layout Option settings |
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6.6 Functional
Clustering |
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6.6.1 Accessing
Functional Clustering options |
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6.6.2 GO Proccess
Order |
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6.6.3 Cluster Gap
Size |
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6.6.4 Turning Functional
Clustering On/Off
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6.6.5 Degree of GO Process
colouring
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| 7. Osprey Preferences and Customization |
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7.1 Graph
Colouring |
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7.1.1
Accessing Graph Colouring |
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7.2 Drawing /
Dragging Graph options |
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7.2.1
Accessing Drawing/Dragging graph options |
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7.3 Node Options |
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7.3.1 Choosing
Method of Colouring Nodes |
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7.3.2 User
Defined Node Colours |
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7.3.3 Colour
Choosing Window |
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7.3.3.1
Swatches tab |
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7.3.3.2 HSB
tab |
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7.3.3.3 RGB
tab |
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7.3.4 Node Size |
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7.4 Edge Options |
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7.4.1 Choosing
Method of Colouring Edges |
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7.4.2 User
Defined Edge Colours |
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7.4.3 Edge Size |
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7.5 Arrow Head Options |
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7.5.1 User
Defined Arrow Head Colour |
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7.5.2 Arrow
Head Size |
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7.6 Label
Options |
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7.6.1 Label
Size |
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7.6.2 Label
Font |
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7.6.3 Label
Style |
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7.6.4 Label
Colour |
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7.6.5 Hiding
Labels |
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7.7 Background
Colour |
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7.7.1
Accessing Background Colour |
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7.8 Saving
Preferences |
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7.8.1 Saving
settings |
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7.8.1.1
Saving Advanced Settings |
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7.8.1.2
Saving Colour Settings |
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7.9 Proxy
Settings |
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7.10 Changing
Databases |
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7.11 Memory
Settings |
| 8. The GRID ( The General Repository of
Interaction Datasets ) |
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8.1 Where to find
The GRID |
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8.2 Osprey and The
GRID |
| A. Known Problems and Common Errors |
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A.1 What to
do if you Encounter an Error |
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A.2 The
Osprey Error Log |
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A.3 Reporting
Errors to the Osprey Team |
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A.4 Known
Problems |
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A.5 Common
Errors |
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A.5.1 Unable
to Install Osprey under a Windows 2000, NT, or XP |
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A.5.2 Unable
to Add Interactions |
| B. Credits |
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B.1 The Osprey Team |
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B.2 The Osprey
Contributors |
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B.3 The Osprey
Supporters |
| C. Future Updates and Obtaining Patches |
| D. Osprey Change History |
| E. Purchasing Osprey Licenses for
Commercial Organizations |
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E.1
Commercial Applications |
