Go to the table of contents

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:

- A) ToolBar: The toolbar places the most commonly used options in osprey at the users fingertips. Options such as saving, zooming, and changing item colour and size are all available via the toolbar.
- B) Gene/Edge Info: This area of the layout displays information queried from The GRID (see section 8. The GRID ( The General Repository of Interaction Datasets)) about a selected node or edge in the network. For a description of what is in this area see section 4.4 Gene/Edge Info Area
- C) Network Filters: These buttons are used to invoke any one of the network filters available to the user (see section 5.1 Filtering Networks)
- D) Connectivity Filters: These buttons are used to invoke any one of the connectivity filters available to the user (see section Connectivity Filters 5.2)
- E) Osprey Menus: All options available in Osprey, can be accessed via these menus. For more information on the specific options available in each menu, see section 4.2 Osprey Menus.
- F) Show Loner Nodes Option: By setting this option to "YES", nodes without interactions stemming from them will be shown on the screen. By setting this option to "NO", nodes with no interactions will be hidden from view.
- G) Network Display Area: This is the area where user defined networks are manipulated. When loading a graph from a file ( or loading from a database ) all nodes and interactions will be displayed here (see section 4.3 Networks).
- H) Status Bar: This area has buttons and statistics that change as the status of the graph changes

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

- New: This option creates a new blank network that can be used to start developing a network from scratch
- Open: Use this menu to access the options for opening one of the many file types recognized by Osprey. For an outline of the files recognized by Osprey, see section 3.1 Types of Files Opened by Osprey. There are two options under open (see figure 4.2.1 - 2):
  - Standard: opens a file that you have previously saved using Osprey.
  - Dataset: opens one of the pre-made datasets included with Osprey (see figure 4.2.1 - 3). These datasets are derived from the set of interactions provided by the General Repository of Interaction Datasets ( see section 8. The GRID ( The General Repository of Interaction Datasets ). You can add your own datasets to this list by saving them as a .osp ( osprey file ) and storing them in the Datasets directory in the Osprey installation directory.

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

Figure 4.2.1 - 3: The Datasets provided with Osprey and Derived from The GRID

- Save: This option is used to save files that have been opened by Osprey, or have been previously saved
- Save As: Use this option to save files that have not been previously saved or you wish to save as an alternative name
- Save Colour Index: Can be used to save the current set of colours used to extenuate annotation within Osprey to SVG, PNG or JPG images (see section 4.6 Saving Colour Indices. There are two options under this menu:
  - Only visible: This saves an image of the colours currently used by osprey. It will only save visible colours, so colours that have been filtered will not be saved.
  - Both Visible and Invisible: This saves an image of the colour index that includes both visible and invisible colours used in annotation on the current graph.

Figure 4.2.1 - 4: The Save Colour Index submenu options

- Save Settings: This option can be used to save options customized by the user for automatic initialization each time that the application is run. There are two options under this menu:
  - Advanced Settings: Advanced Settings include all the settings in the Advanced Settings Menu as well as all user defined node, edge, labels, arrow sizes and colours. This option will take all these settings and will initialize Osprey with them each time the application is run.
  - Colour Settings: Colour Settings are all the colour index settings in the Go Process index, Experimental Colour index and Source index. By changing colour settings, you will affect only the colours on the network when colouring the graph by user defined colours mode, see section 7.1 Graph Colouring. When colouring by default or by Osprey File Colours, these colour settings will not apply.

Figure 4.2.1 - 5: The Save Settings submenu options

- Print: This option will take the graph currently displayed in the Network Display Area, and print the graph to a printer attached to your computer.
- Superimpose: "To lay or place (something) on or over something else" [http://www.dictionary.com/search?q=Superimpose]. The superimpose option will allow for overlaying additional files onto an existing network in Osprey. There are two options under this menu:
  - Standard: Superimposes any one of the three recognized file formats. See section 3.1 Types of Files Opened by Osprey for details.
  - Dataset: Superimposes one of the pre-made datasets included with Osprey (see figure 4.2.1 - 3). These datasets are derived from the set of interactions provided by the General Repository of Interaction Datasets ( see section 8. The GRID ( The General Repository of Interaction Datasets ). You can add your own datasets to this list by saving them as a .osp ( osprey file ) and storing them in the Datasets directory under the Osprey installation directory.

Figure 4.2.1 - 6: The Superimpose submenu

Figure 4.2.1 - 7: The Datasets provided with Osprey and Derived from The GRID available for Superimposing

- Export: Use this option to take the current network displayed by Osprey and save it to an image for incorporation into figures, or for viewing and manipulation in other applications, such as Adobe Photoshop or Macromedia Fireworks. Osprey can currently export to SVG, JPG, or PNG images.
- Work Offline: This option is available for those users who do not have a readily available connection to the internet. Note:working offline will limit your options within Osprey.
- Exit Osprey: This menu option will exit the application

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

- Copy Screen Names: Click on this option to copy all the currently selected screen names to the systems clip board.
- Copy Node Info: Selecting this menu item will copy all the annotation information for the selected genes to the systems clip board.
- Copy Edge Info: This option will copy all the edge info for all the selected edges to the systems clip board.
- Copy Neighboring Edges Info of selected Nodes: When clicked this will copy any Edge info of the selected node/s to the systems clip board.
- Select All: Click on this option to select all of the vertices and edges currently visible on the network.
- Invert Selected Nodes: Selecting this menu item will select all the nodes that are not currently selected and unselect all the currently selected nodes.
- Crop White Space: This option will get rid of all excess white space around the graph and will move the graph to the upper left to save the most space on the Network Display Area.
- Fit to Screen: When clicked this will adjust the zoom percentage (between 25% - 125%) to best fit the network completely on your current screen.
- Zoom In: This will make the network appear larger on the screen increased by 1%.
- Zoom Out: This will make the network appear smaller on the screen decreased by 1%.
- Lock Nodes: This option will take all of the selected nodes on the graph, and will lock them in place so that they are unaffected by automatic layout procedures such as Automatic Relax.
- Unlock Nodes: Use this feature to take any nodes that have been locked in place and allow them to be moved by automatic layout procedures.
- Remove Nodes: This will take any nodes currently highlighted in the network and permanently remove them.
- Remove Edges: This will take any edges currently highlighted in the network and permanently remove them.
- Find: This will search for a node by its gene name, orf name or screen name.
- Update Node Annotation: This will connect to the GRID and download the latest Node Annotations, see section 4.4.4 Update Annotation.
- Change Database: This will allow the user to change between different databases, see section 4.7.1 Changing Databases.

Figure 4.2.2 - 2: The Osprey Change Database Default 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

- Colour Indexes: The Colour indexes submenu contains options for viewing each of the colour sets used for annotation on nodes and edges in Osprey. There are three options under this menu:
  - Experimental Systems: Choosing this colour index will show a listing of colours used to describe experimental system annotation on edges. It also provides the ability to manipulate these colours.
  - Sources: Choosing this colour index will show a listing of colours used to describe source annotation on edges. It also provides the ability to manipulate these colours.
  - GO Process: Choosing this colour index will show a listing of colours used to describe GO Process annotation on nodes. It also provides the ability to manipulate these colours.

Figure 4.2.3 - 2: The Colour Indices Submenu

- Toolbars: The toolbars submenu contains options for viewing the Standard Buttons toolbar and the Status Bar. There are two options under this menu:
  - Standard Buttons: When this option is checked, the toolbar at the top of Osprey will be visible. When it is not checked, the toolbar will be invisible providing additional room for the Network Display Area.
  - Status Bar: When this option is checked, the status bar at the bottom of Osprey will be Visible. When it is not checked, the status bar will be invisible providing additional room for the Network Display Area.

Figure 4.2.3 - 3: The Toolbars Submenu

- Loner Nodes: The loner nodes submenu contains options for turning the loner nodes filter on or off making nodes without edges visible or invisible. There are two options under this menu.
  - Show: When this option is selected, it will turn the Loner Nodes filter off, which will show all nodes on the screen, regardless of the number of interactions stemming from them
  - Hide: When this option is selected, it will turn the Loner Nodes filter on, which will hide nodes on the screen with zero interactions stemming from them.

Figure 4.2.3 - 4: The Loner Nodes Submenu

- Drawing Options: An Osprey network is in drawing mode, when the graph is stationary, and no nodes are currently being moved around the screen. There are four options under this menu.
  - Nodes: By clicking this option you can specify whether or nodes are displayed while in Drawing mode.
  - Edges: By clicking this option you can specify whether or edges are displayed while in Drawing mode.
  - Labels: By clicking this option you can specify whether or labels are displayed while in Drawing mode.
  - Arrows: By clicking this option you can specify whether or arrows are displayed while in Drawing mode.

Figure 4.2.3 - 5: The Drawing Options Submenu

- Dragging Options: An Osprey network is in dragging mode whenever a single node, or a group of nodes are being dragged about the network display area. There are four options under this menu.
  - Nodes: By clicking this option you can specify whether or nodes are displayed while in dragging mode.
  - Edges: By clicking this option you can specify whether or edges are displayed while in dragging mode.
  - Labels: By clicking this option you can specify whether or labels are displayed while in dragging mode.
  - Always: By clicking this option you can specify whether the above three options are drawn for all nodes or for only the ones currently being dragged.

Figure 4.2.3 - 6: The Dragging Options Submenu

- Network Statistics: This option will show several statistics about the currently displayed network.

Figure 4.2.3 - 7: Network Statistics

- Selected Node Report: This option will display all gene info about the currently selected nodes

Figure 4.2.3 - 7: Selected Gene Report

- View All Comments: This option will display all comments that have been made on any nodes currently in the Network Display Area.

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

- All Interactions for Selected Nodes: This option will query The GRID and retrieve all interactions stored for the currently selected nodes.
- Only Interactions within Selected Nodes: This option will query The GRID and retrieve all interactions stored that are contained only within the selected set of nodes.
- New Node: This option provides the ability to add individual nodes manually by name.
- New Interaction: This option allows for manual addition of interactions between nodes currently in the network.

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

- Nodes: The nodes submenu has options that affect nodes; specifically colour and size
  - Colour: This options provides the ability to change the selected nodes' colour
  - Size: This options provides the ability to change the selected nodes' size

Figure 4.2.5 - 2: The Nodes Submenu

- Edges: The edges submenu has options that affect edges; specifically colour and size
  - Colour: This options provides the ability to change the selected edges' colour
  - Size: This options provides the ability to change the selected edges' size

Figure 4.2.5 - 3: The Edges Submenu

- Arrows: The edges submenu has options that affect arrows; specifically colour and size
  - Colour: This options provides the ability to change the selected arrow heads' colour
  - Size: This options provides the ability to change the selected arrow heads' size

Figure 4.2.5 - 4: The Arrows Submenu

- Text: The edges submenu has options that affect labels; specifically colour, font, and visibility
  - Colour: This options provides the ability to change the selected labels' colour
  - Font: This options provides the ability to change the selected labels' font, size and style
  - Show: When this is clicked, it makes selected labels visible
  - Hide: When this is clicked, it makes selected labels not visible

Figure 4.2.5 - 5: The Text Submenu

- Background Colour: This provides the ability to change the graph's background colour
- Advanced Settings: This has all other options and settings that were not mentioned above, such as layout settings and colouring modes

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

- Network Filters: These filters, filter the nodes on the graph depending on network features such as Experimental System, Source and Go Process. Note: Only the Currently viable filters will be enabled. To change the available filters change the colouring mode (see section 5. Filters for more detail)
  - Experimental System: Select this option to invoke the Experimental System Filter
  - Source: Select this option to invoke the Source Filter
  - Go Process: Select this option to invoke the Gene Ontology Process Filter
  - Turn off Filters: This option turns off a network filter, if one of them is turned on

Figure 4.2.6 - 2: The Network Filters Submenu

- Connection Filters: These filters filter the nodes on the graph depending on the number of connections they have with each other
  - Minimum: Select this option to invoke the connection minimum filter, it will only keep nodes with a chosen minimum amount of connections before any nodes are removed
  - Iterative Minimum: Select this option to invoke the iterative connection minimum filter, it is similar to the above filter except it only keeps nodes with a chosen minimum amount of nodes after all nodes are removed
  - Depth: Select this option to invoke the connectivity depth filter, it keeps nodes that are a chosen number of connections deep from the selected nodes
  - Turn off Filters: This option turns off any connection filters if any were turned on

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

- Auto Relaxation: This submenu has the relaxation algorithm which attempts to relax the the graph by separating all the nodes and edges.
  - Start Relaxation: Use this option to begin automatic relaxation on all of the nodes currently selected in the network.
  - Stop Relaxation: When Relaxation is in progress, Start Relaxation will be replaced by Stop Relaxation; click it to stop the nodes from relaxing.

Figure 4.2.7 - 2: The Auto Relaxation Submenu

- Circular: This submenu has the circular layouts, you can choose from.
  - One Circle: This option places all the selected nodes in a circle whose size is proportionate to the size of the selection box.
  - Concentric Circles: This option places all the selected options in concentric circles.
  - Concentric Circle Options: This option gives the user the ability to change the number of rings as well as the capacity of rings to achieve the best fit.

Figure 4.2.7 - 3: The Circular Submenu

- Dual Ring: The following two layouts split the nodes into two groups, highly connected nodes in and highly connected nodes out.
  - Highly Connected In: This option places all the highly connected nodes in the inner circle and all other nodes in the outer circle.
  - Highly Connected Out: This option places all the highly connected nodes in the outer circle and all other nodes in the inner circle.

Figure 4.2.7 - 4: The Dual Ring Submenu

- Spokes: This submenu gives the user two methods of bringing all the nodes connected to a selected nodes into a spoke layout
  - Default: This option makes sure that the spoke does not disturb the current look of the graph, it only brings in nodes that are not currently in the center of a spoke layout or in between two or more spoke layouts.
  - Forced: This forces all nodes that are connected to the selected nodes to come in to the spoke layout.
  - Spoke Options: This offers the user a way of adjusting how many nodes go into each ring and how large each ring of the spoke layout is

Figure 4.2.7 - 5: The Spokes Submenu

- Global: This submenu has algorithms that act on the entire graph, disregarding whether or not nodes are selected or locked
  - Spoked Dual Ring: This is a global layout that attempts to place a large number of nodes into two rings of spokes layouts with the most highly concentrated spokes on the inside ring and the least concentrated spokes layouts in the outer ring
  - Spoked Dual Ring Options: This option allows the user to adjust the parameters that the spoked dual ring layout uses to determine which hubs go in which ring and how large every hub is.

Figure 4.2.7 - 6: The Global Submenu

4.2.8 Help Menu

Figure 4.2.8 - 1: The Osprey Help Menu

- Help Manual: This option calls the help manual that you are currently reading.
- Check for Updates: This option goes to the osprey web site and checks to see if the version of Osprey you are using is the latest one or not.
- About: Use this option to view information about Osprey, including Osprey developers and version information.

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:

- B) Specific Gene Info: At the top of the area, specific information about the gene is displayed. In the table on the left hand side, ORF names and Gene/Alias Names are displayed. On the right hand side, a zoomed in image of the node itself is displayed. This zoomed in node will show the colours it currently represents.
- C) Get New Interactions Button: Clicking this button will query the database, and retrieve a list of interactions involving the selected node that are not currently displayed in the Network Display Area. See section 4.5 Adding Interactions for more information about adding interactions.
- D.) Ability to change the current screen name.
- E.) Allows the user to add comments to any selected gene.
- F) Description: This section displays a plain text description of the currently selected node. This description will be retrieved from the underlying database.
- G, H, I) Gene Ontology Information: These three sections display the three major categories used by the Gene Ontology Consortium. Namely, Go Component, Go Process, and Go Function respectively. The specific categories corresponding to the selected node are shown in this area.
- J) Gene Ontology Special: This section of the Gene/Edge Info area shows the Gene Ontology Special categories used for this gene. GO Special categories are the ones used for colouring of nodes.

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:

- B) Interacting Genes: At the top of the Gene/Edge Info area, when an edge is selected, information about genes participating in an interaction will be shown. Information such as the ORF names and Gene/Alias names will be displayed.
- C) Experimental System / Sources: This table shows the various experimental systems and sources that correspond to the selected edge. Although the edges will not be coloured by both simultaneously ( see section 7.1 Graph Colouring ) this table will still reflect both sets of information.
- D) PubMed ID: A link to any PubMed listing on a given interaction.

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

> > - Select a node (or several nodes as described above in section 4.3.2.4 Selecting Multiple Nodes)
> > - Click on the Edit Osprey Menu
> > - Click on Remove Nodes

> > Figure 4.3.2.6 - 1 Remove Nodes on Edit Menu Bar

> 2.) Right-Click Menu

> - Select a node (or several nodes as described above in section 4.3.2.4 Selecting Multiple Nodes)
> - Right-click on an empty area of the Graph
> - Click on Remove Node

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

> > - Select an edge (or several nodes by holding the ctrl button and clicking on all the desired edges)
> > - Click on the Edit Osprey Menu
> > - Click on Remove Edges

> > Figure 4.3.2.7 - 1 Remove Edges on Edit Menu Bar

> 2.) Right-Click Menu

> - Select an edge (or several nodes by holding the ctrl button and clicking on all the desired edges)
> - Right-click on an empty area of the Graph
> - Click on Remove Edges

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

> - Click on the "View" menu in the Menu Bar
> - Click on the "Loner Nodes" submenu
> - Select either the Show or Hide radial button

Figure 4.3.2.8 - 1 Loner Nodes Submenu

> > 2.) The Status Bar button

> - If the button says "Loner Nodes? Yes" it means they are visible
> - If the button says "Loner Nodes? No" it means they are invisible
> - Click on the button to change its status

> Figure 4.3.2.8 - 2 Loner Nodes 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:

- Insert All Interactions for Selected: This option will query The GRID and bring in all nodes that have an edge with currently selected Nodes.
- Insert Only Interactions within Selected: This option will query The GRID and bring in all edges that can currently go between selected nodes.
- One Circle Layout: This will place all selected nodes into a circle.
- Concentric Circle Layout: This will place all selected nodes into concentric circles.
- Create Default Spoke: This option will bring all nodes that are connected to currently selected nodes into spoke layouts without disturbing the graph (it will leave nodes that are in the center of other spokes layouts and spokes that are shared between two or more spoke layouts untouched).
- Create Default Spoke: This option will bring all nodes that are connected to currently selected nodes into spoke layouts disregarding where these nodes were before.
- Spoked Dual Ring Layout: This is a global layout that will attempt to place a large amount of nodes into an easily manageable layout.
- Lock Nodes: This option will lock any selected genes in place, so that they will not be affected by any layout algorithm (except the global ones).
- Unlock Nodes: This option will unlock any locked selected genes, allowing their position to be manipulated by all layout algorithms.
- Remove Nodes: This option will permanently remove any selected nodes from the network. See section 4.3.2.6 Removing Nodes for more details.
- Remove Edges: This option will permanently remove any selected edges from the network. See section 4.3.2.7 Removing Edges from more detail.

4.4 Gene/Edge Info

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

- If the gene is known as the one in figure 4.4 - 1 all the data about this gene will be displayed in this section
- If the data is not know or if the added gene is a custom gene this area will not display much information as in figure 4.4 - 2

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:

- Click on the desired node
- Click on the text box under the Screen Name label (shown below in Figure 4.4.1 - 1)

Figure 4.4.1 - 1 Screen Name

- Type in the desired name.
- Then Click on Change.
- The change will be reflected on the graph, but nothing in the database or the gene info will change (shown below in Figure 4.4.1 - 2).

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:

- Click on the desired gene.
- Click on the "Add Comment" button.

Figure 4.4.2 - 1 Add Comment Button

- A window will pop-up for you to type your comment in.

Figure 4.4.2 - 2 Add Comment window

- After adding your comment click on the "Add Comment" button.
- To close the comment window without making any changes click on close.
- The original "Add Comment" button on the Gene/Edge Info area will change to "View Comment" to reflect the fact that there is a comment saved now.

Figure 4.4.2 - 3 View Comment Button

- To view, edit or remove the comment click on the View Comment button.

Figure 4.4.2 - 4 View Comment Window

- To modify the comment, type in the desired modifications then click on the "Update Comment" button.
- To remove the comment completely click on the "Remove Comment" button.
- To close the comment without making changes click the close button.

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:

- Select the desired nodes.
- From the Main Menu bar select the "Selected Node Report" menu item under the view menu.

Figure 4.4.3 - 1 Selected Node Report menu item

- Click on it and a report window will appear

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:

- Click on the "Edit" Menu in the Menu Bar
- Click on Update Node Annotation

Figure 4.4.4 - 1 Update Node Annotation

- A warning message will appear asking you if you are sure you want to do this (it may take a long time if you have a slow internet connection)

Figure 4.4.4 - 2 Update Note Annotation Warning

- If you click Update Osprey will connect to The GRID and update your annotation

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:

- The Orf Info Area
- The Network Display Area Command Menu (Right-click menu)
- The Edit Menu

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:

- A) ORF: This field shows the orf name of any other orfs interacting with the selected node.
- B) Gene: This field shows some of the common gene names and aliases for other genes that interact with the selected node.
- C) System: This field shows the experimental system that was used to derive the particular interaction.
- D) Source: This field shows the source that reported this interaction within the support database.

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)

> > - Select the desired nodes (for more info on selecting nodes see section 4.3.2.1 Selecting Nodes)
> > - Right-click in an empty area of the graph to bring up The Network Display Command Menu
> > - Click on Insert All Interactions for Selected as shown below in Figure 4.5.2.1 - 1

> > 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)

> > - Select the desired nodes (for more info on selecting nodes see section 4.3.2.1 Selecting Nodes)
> > - Right-click on an empty area of the screen
> > - Click on "Insert Only Interactions within" as shown in Figure 4.5.2.2 - 1

> > Figure 4.5.2.2 - 1: A set of nodes with no interactions shown

> > Figure 4.5.2.2 - 2: same image as 4.5.2.2 - 1 but with all interactions within the selected nodes inserted

> > Notice how only interactions involving only the selected nodes were added to the network. No new nodes are ever added when using this option. This can be very powerful for determining connections between a core set of nodes in the network.

> > 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 in the Menu Bar
> > - Click on "Only interactions within Selected Nodes" as shown in Figure 4.5.2.2 -3

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:

- Go Process Index: Shows colours for each of the GO Process categories currently displayed on the Network and used to colour the individual nodes on the graph.
- Experimental Systems Index: Shows colours for each of the Experimental Systems currently displayed by Osprey and used to colour the edge segments when the graph is in Colour By Experimental System Mode ( see section 7.1 Graph Colouring for more details )
- Sources Index: Shows colours for each of the Sources currently displayed by Osprey and used to colour the edge segments when the graph is in Colour By Source Mode ( see section 7.1 Graph Colouring for more details )

To access the various colour 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:

- Click on the Osprey "File" Menu
- Click on the "Save Colour Index" submenu
- Choose either to save "Only Visible" colours or "Both Visible and Invisible" Colours

Figure 4.6.4 - 1: The Save Color Index Menu

- This option will then ask you for a location and format for which to save the index. ( see figure 4.6.4 - 2 )

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

- Choose a destination to save the file, and type a name for the index and click save to create the index. For an example of a colour index for an arbitrary network, see the following figure ( figure 4.6.4 - 3 )

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 May 01, 2003 Osprey supports the following four major organisms:
1.) Yeast (Saccharomyces cerevisiae)
2.) Human (Homo sapiens)
3.) Mouse (Mus musculus)
4.) Fly (Drosophila melanogaster)
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.
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.

4.7.1 Changing Databases

By default Osprey will connect to the yeast database, if you want Osprey to default to a different database you can simple connect to the database of interest and save your settings, see section 7.8 Saving Preferences for more details. In order to change to a different database select the "Database" menu, see figure 4.7.1-1.

Figure 4.7.1 - 1: Change Database Menu

The title at the very top of the Osprey application will let you know what database you are currently connected to without having to go the the "Database" menu, see figure 4.7.1-2, and 4.7.1-3 for examples.
Figure 4.7.1 - 2: Osprey currently connected to the "Yeast GRID" which contains the yeast database
Figure 4.7.1 - 3: Osprey currently connected to the "Fly GRID" which contains the fly database

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

Go to the table of contents