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4. Basic Introduction

This section provides an introduction to Osprey, showing the overall layout of the application as well as how to do many simple tasks.  This section assumes that you already have Osprey installed on your computer, and it is available for you to use.  If this is not the case, please refer to section 2. Osprey Installation.

This section also assumes that you are able to launch the Osprey Network Visualization System and that you are familiar with procedures for opening Osprey files.  If you are unfamiliar with these procedures, please see section 3. Opening and Saving Files

4 .1 Osprey Layout

The following is a description of the major sections comprising the Osprey layout:

Figure 4.1 - 1: A Blank Layout of Osprey after the application has been launched

4 .2 Osprey Menus

Osprey is a menu driven application. By accessing the collection of options stored under the different menu headings, Osprey provides the tools necessary for manipulation and analysis of the networks. All options available to the user can be accessed via the Osprey menus, even though some options may have methods of access outside of the Menu bar. The following sections will outline briefly the options available in each of Osprey's menus.

Figure 4.2 - 1: This is an isolated view of the menus available in Osprey

4.2.1 File Menu

The Osprey File Menu contains many of the options for writing to files, as well as opening from files. The following is a listing of each of the options available in the file menu, with a brief description of what service the option provides.

Figure 4.2.1 - 1: The Osprey File Menu

Figure 4.2.1 - 2: The Options available in the Osprey File Menu

Figure 4.2.1 - 4: The Save Colour Index submenu options

Figure 4.2.1 - 5: The Save Settings submenu options

Figure 4.2.1 - 6: The Superimpose submenu

4.2.2 Edit Menu

The Osprey edit menu contains many options for manipulating a currently displayed graph. The following is a listing of each of the options available in the edit menu, with a brief description of what service the option provides:

Figure 4.2.2 - 1: The Osprey Edit Menu



4.2.3 View Menu

The View Menu provides a variety of options for changing the look and feel of the currently displayed graph. The following is a listing of each of the options available in the view menu, with a brief description of what service the option provides:

Figure 4.2.3 - 1: The Osprey View Menu

Figure 4.2.3 - 2: The Colour Indices Submenu

Figure 4.2.3 - 3: The Toolbars Submenu

Figure 4.2.3 - 4: The Loner Nodes Submenu

Figure 4.2.3 - 5: The Drawing Options Submenu

Figure 4.2.3 - 6: The Dragging Options Submenu

Figure 4.2.3 - 7: Network Statistics

Figure 4.2.3 - 7: Selected Gene Report

 

4.2.4 Insert Menu

The insert menu provides several options for adding additional information, such as interactions and nodes, to a currently displayed network. The following is a listing of each of the options available in the insert menu, with a brief description of what service the option provides:

Figure 4.2.4 - 1: The Osprey Insert Menu

4.2.5 Format Menu

The format menu provides several options for adding additional information, such as interactions and nodes, to a currently displayed network. The following is a listing of each of the options available in the insert menu, with a brief description of what service the option provides:

Figure 4.2.5 - 1: The Osprey Format Menu

Figure 4.2.5 - 2: The Nodes Submenu

Figure 4.2.5 - 3: The Edges Submenu

Figure 4.2.5 - 4: The Arrows Submenu

Figure 4.2.5 - 5: The Text Submenu

4.2.6 Filters Menu

The filters menu has the same functionality as the buttons in the bottom left hand corner window. It offers access to the Network filters which filter the graph depending on network features such as Source or Experimental System, and Connection filters which filter the graph depending on number of connections each node has.

Figure 4.2.6 - 1: The Filters Menu

Figure 4.2.6 - 2: The Network Filters Submenu

Figure 4.2.6 - 3: The Connection Filters Submenu

4.2.7 Layout Menu

This menu offers all the different ways to layout nodes in an Osprey Network. It ranges from the relax algorithm to a simple circular layout to a more advanced Dual Spoked Ring Layout that attempts to display up to 1500 - 2000 nodes in a easily manageable format. See section 6. Layouts for more details on layouts

Figure 4.2.7 - 1: The Osprey Layout Menu

Figure 4.2.7 - 2: The Auto Relaxation Submenu

Figure 4.2.7 - 3: The Circular Submenu

Figure 4.2.7 - 4: The Dual Ring Submenu

Figure 4.2.7 - 5: The Spokes Submenu

Figure 4.2.7 - 6: The Global Submenu

4.2.8 Help Menu

Figure 4.2.8 - 1: The Osprey Help Menu

4.2.9 Database Menu


Figure 4.2.9 - 1: The Osprey Database Menu


4.3 Networks

In this section, we will examine a simple Osprey network and some of the options that accompany them.

Figure 4.3 - 1: A Simple Example Network

4.3.1 Network Display Area

Figure 4.3.1 - 1: The Network Display Area

The Network Display Area (NDA) is the most powerful section of the Osprey application.  The NDA is used to display all information regarding nodes and interactions.  Here, nodes are represented by colourful circles, and interactions/edges are represented by colourful lines. Interactions can be shown using user defined, experimental system, or sources to determine colouring (see section 7. Osprey Preferences and Customization).  Nodes can be shown using user defined, or Gene Ontology Process categories to determine colouring (see section 7. Osprey Preferences and Customization).  Any interactions removed or added to Osprey, are displayed in this area. 

The NDA provides many options for working with networks.  By left-clicking on a node or an edge using a mouse, the node or edge will be selected.  Selected nodes can be dragged and placed anywhere within the Network Display Area.  For more information on manipulating networks, see section 4.3.2 Manipulating the Network .

4.3.2 Manipulating the Network

There are many ways that a network can be manipulated using Osprey. This includes basic things such as moving individual nodes and selecting and moving groups of nodes to options like removing nodes and edges.

4.3.2.1 Selecting Nodes

Figure 4.3.2.1 - 1: Network with a single node selected

When a single node is clicked on in the Network Display Area, that node becomes highlighted ( i.e. (A) in Figure 4.3.2.1 - 1 ).  A selected node will have additional database information displayed about it, as soon as it is clicked.  This information will be shown in the Gene/Edge info area on the left hand side of Osprey.  The following describes briefly the information shown in the Gene/Edge Info area for a selected node:

4.3.2.2 Selecting Edges

Figure 4.3.2.2 - 1: Network with a single edge selected

When a single edge is clicked on in the Network Display Area, that edge becomes highlighted ( ie. (A) in Figure 4.3.2.2 - 1 ).  A selected edge will have additional database information displayed about it, as soon as it is clicked.  This information will be shown in the Gene/Edge info area on the left hand side of Osprey.  The following describes briefly the information shown in the Gene/Edge Info area for a selected edge:

Note: Selecting multiple edges can be done by holding the ctrl button and clicking on all the desired edges

4.3.2.3 Moving Individual Nodes

By clicking and holding the left mouse button on a single node, you can drag a node to different places on the screen.  This may take a little practice as it requires a little bit of coordination.  This technique is ideal for placing nodes in a format that makes networks suitable for use as published figures.

4.3.2.4 Selecting Multiple Nodes

Figure 4.3.2.4 - 1: Our tutorial network with a box being dragged to select multiple nodes

Osprey also allows for selecting of multiple nodes in the network.  This is done by encompassing the nodes in a selection rectangle.  To encompass the nodes in a selection rectangle, simply left click and hold the mouse button in an unoccupied area of the Network Display Area ( ie. One with no nodes or edges ) and drag the resulting rectangle until the nodes you want selected are all inside the rectangle ( ie. (A) in the above figure 4.3.2.4 ).  When you release the mouse button, all of the nodes inside the rectangle will be selected.

Note: The other way to select nodes is to hold the ctrl button on your keyboard while clicking on the nodes you would like to select.

4.3.2.5 Moving Multiple Nodes

With multiple nodes selected ( see section 4.3.2.4 Selecting Multiple Nodes ) simply left-click and hold the mouse button on any one of the selected nodes.  While holding the mouse, you can drag the entire group of selected nodes and place them anywhere in the Network Display Area.

4.3.2.6 Removing Nodes

Follow these steps to remove a node (and all its edges). There are currently two ways of doing this:

1.) The Menu Bar

2.) Right-Click Menu

 

Figure 4.3.2.6 - 2 Remove Nodes Right-click menu

4.3.2.7 Removing Edges

Follow these steps to remove an edge. There are currently two ways of doing this:

1.) The Menu Bar

2.) Right-Click Menu

 

Figure 4.3.2.7 - 2 Remove Edges Right-click menu

4.3.2.8 Showing Loner Nodes

Loner nodes are nodes that do not have any edges coming out of them (or into them). They can either be left visible, or removed from the graph and set to invisible.

There are currently two ways of changing the visibility option of loner nodes:

1.) The Menu Bar

 

Figure 4.3.2.8 - 1 Loner Nodes Submenu

2.) The Status Bar button

 

4.3.3 Network Display Area Command Menu

Figure 4.3.3 - 1: Image of all the possible options on the Network Display Area Command Menu

The Network Display Area Command Menu can be launched by right-clicking anywhere in the Network Display Area.  Depending on whether nodes or edges have been selected, the options available on the command menu may vary.  Each of these options is outlined as follows:

4.4 Gene/Edge Info

The Gene Info Area displays information about the selected node. This information is obtained from the Grid database.

Figure 4.4 - 1 Gene Info for CLN2

Figure 4.4 - 2 Gene Info for CLN5 (unknown)

 

4.4.1 Changing Screen Name

To change the name of a selected node on your graph follow these steps:

Figure 4.4.1 - 1 Screen Name

Figure 4.4.1 - 2 Change Screen Name

4.4.2 Adding Comments

Osprey offers the option of adding comments to selected genes that can be viewed and updated as needed.

Follow these steps to add a comment:

Figure 4.4.2 - 1 Add Comment Button

 

Figure 4.4.2 - 2 Add Comment window

Figure 4.4.2 - 3 View Comment Button

 

Figure 4.4.2 - 4 View Comment Window

 

4.4.3 Viewing Selected Node Report

You can view the gene info for two or more genes in a report like table. Follow these steps to find out how:

Figure 4.4.3 - 1 Selected Node Report menu item

Figure 4.4.3 - 2 Selected Nodes Report Window

Note: This table can be copied and pasted into a spread sheet program (using the ctrl+c and ctrl+v hotkeys), but this option is not endorsed by this program.

4.4.4 Update Annotation

This option will connect to the GRID database and may change the annotation of your layout to the latest annotations available: Follow these steps to call this function:

Figure 4.4.4 - 1 Update Node Annotation

Figure 4.4.4 - 2 Update Note Annotation Warning

4.4.5 Edge Info

If you click on an edge, the Gene/Edge Info area will show you the edge info. It will display the node's given Gene and ORF names as well as Experimental System, Source info, and any PubMed links.

4.5 Adding Interactions

The ability to incorporate new interactions into an already existing network is one of the most powerful features that Osprey has to offer. Interactions can be added to the graph from a large selection available in Ospreys underlying support database ( see section 8 The GRID ( The General Repository of Interaction Datasets ) ). 

There are three major areas of Osprey that can be used to add new interactions.  Namely:

4.5.1 From the Orf Info Area

Figure 4.5.1 - 1 Orf Info Area

The gene info area is used to display additional information about a selected orf in the Network Display Area.  In addition to this, it also provides a button that allows for the incorporation of new interactions into the already established graph.  To get this process started, simply highlight a node on the graph, and click the "GET NEW INTERACTIONS" button on the Gene Info Area.  When this button is clicked, a window with a listing of new interactions is launched:

Figure 4.5.1 - 2: An example listing of additional interactions for a selected orf in a network

This listing of interactions has several key areas crucial to deciding which interactions you want to add to the existing network:

You can select any of the interactions listed on this screen by clicking on them with the left-mouse button.  To select multiple interactions, simple click and hold the left mouse button and drag through the list to select as many interactions as desired.  Once you have selected interactions, you can add them by clicking on the "Add Selected Interactions" button ( pictured as (E) in Figure 4.5.1 - 2 ).  This will take these new interactions and incorporate them into the network currently stored in the Network display area. 

If, at any time, you simply want to add all interactions available in the listing, click the "Add All Interactions" button ( pictured as (F) in Figure 4.5.1 - 2 ).

4.5.2 From the Network Display Area Command Menu and Insert Menu

The Network Display Area Command Menu and the edit menu offers two easy methods for incorporating new interactions into a network:

1.) Adding all interactions to selected vertices (section 4.5.2.1 Adding all interactions to selected vertices).

2.) Adding only interactions within Selected Vertices (section 4.5.2.2 Adding only interactions within Selected Vertices).

 

4.5.2.1 Adding all interactions to selected vertices

You can add ALL interactions to a single node or several nodes in two different ways:

1) Using The Network Display Area Command Menu (Right-click menu)

Figure 4.5.2.1 - 1: A set of selected nodes with the Network Display Area Command Menu open

By clicking on the "Insert All Interactions for Selected" option, all interactions stored in the underlying database for ALL of the selected vertices will be added to the network. 

 

Figure 4.5.2.1 - 2:  Figure 4.5.2.1 - 1 after "Insert All Interactions for Selected" has been applied to the selected nodes

 

2) Using The Insert Menu

    • Select the desired nodes (for more info on selecting nodes see section 4.3.2.1 Selecting Nodes)
    • Click on the Insert menu from the Menu bar
    • Click on All Interactions for Selected Nodes (as shown in Figure 4.5.2.2 - 3)

    Figure 4.5.2.2.3 Insert Menu

4.5.2.2 Adding only interactions within Selected Vertices

This is one of the most popular options for retrieving new interactions, and one that is rarely seen in other network display systems.  With this option, one can retrieve interactions that exist ONLY within a set of nodes in a network. There are 2 ways to access this feature:

 

1) Using The Network Display Area Command Menu (Right-click menu)

2) Using The Insert Menu

Figure 4.5.2.2 - 3: Insert Menu, Only interactions within Selected Nodes

4.6 Colour Indices

Colour indices show a mapping of colours used in a network to their meaning.  There are three major colour indices used by Osprey when displaying a network:

To access the various colours indices, please refer to the windows menu ( see section 4.2.5 Windows Menu )

4.6.1 Go Process Index

 

Figure 4.6.1 - 1: An example of a GO Process Index for a given network

The GO Process Index describes the various colours used on the individual nodes to represent Special GO Process categories.  These colours are completely customizable, and can be changed simply by clicking on the "Change Colour" button behind any particular Go Process category.

4.6.2 Experimental Systems Index

 

Figure 4.6.1 - 1: An example of an Experimental Systems Index for a given network

The Experimental Systems Index describes the various colours used on the individual edge segments used to represent the different experimental systems.  These colours are completely customizable, and can be changed simply by clicking on the "Change Colour" button behind any particular experimental system in the index.

4.6.3 Sources Index

 

Figure 4.6.1 - 1: An example of a Sources Index for a given network

The Sources Index describes the various colours used on the individual edge segments used to represent the different sources of interactions.  These colours are completely customizable, and can be changed simply by clicking on the "Change Colour" button behind any particular source in the index.

4.6.4 Saving Colour Indices

These three colour indices can also be saved as either a JPG, PNG, or SVG images so that they may be incorporated into figures or other projects outside of Osprey itself.  Follow these steps to save the Colour Indices:

 

Figure 4.6.4 - 1: The Save Color Index Menu

 

Figure 4.6.4 - 2: The File Chooser for saving a color index

 

Figure 4.6.4 - 3: An example Colour Index for an Arbitrary Network


4.7 Multiple Organism Support

New to Osprey version 1.0.0+ is the ability access different databases containing annotation information from several different organisms. As of Feb, 2004 Osprey supports the following organisms:

    1.) Yeast (Saccharomyces cerevisiae)
    2.) Human (Homo sapiens)
    3.) Mouse (Mus musculus)
    4.) Fly (Drosophila melanogaster)
     5.) S. Pombe (Schizosaccharomyces pombe)
    6.) Worm (C. Elegans)
    7.) Rat (Rattus norvegicus)
    8.) Zebra Fish (Danio rerio)
   
All of the above databases are maintained by the GRID, which receives their information from several different sources including SGD, NCBI, and Locus Link. See http://biodata.mshri.on.ca/grid for more information. See section 7.10, "Changing Databases" for information on the various ways to change the database Osprey connects to.

Note: This option allows the more ambitious Osprey user to create a MySQL database to maintain a private version of interaction data. For more information on this option please contact the Osprey administrators for more details, ospreyadmin@mshri.on.ca.  


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

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