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7. Osprey Preferences and Customization

This section will describe several options that are available for customization within Osprey. These options include the following:

- Ability to change sizes and colours of most Osprey objects such as edges, nodes, labels, and arrow heads.
- Ability to change background colours

7.1 Graph Colouring

The graph can be coloured by three different methods. These methods change the colours used by Osprey to colour a network. A graph can be coloured by one of the following methods:.

- Default Colours: Colouring by default colours will change the network colours, including colours for experimental systems, sources, and the background, to the default colour as defined by Osprey. Use this option if you want to view the colours as defined originally by the application developers.
- User Defined Colours: Colouring by user defined colours, will colour the displayed network via the colours customized from within the application itself. These are the colours that are manipulated within the Osprey application, and are saved to the preferences file.
- Osprey File Colours: Osprey File Colours, are the colours stored within an Osprey save file. If Osprey is set to colour by file, the current network will be coloured to reflect the colours stored within the currently opened Osprey file.

Note: By selecting the "Always default to colouring by Osprey File" checkbox, Osprey will colour opened networks by the colours stored within the file by default. If this option is not selected, Osprey will default to colouring based on user defined colours.

Figure 7.1 - 1: The Osprey advanced settings menu, with the Colouring Graph option highlighted.

7.1.1 Accessing Graph Colouring

The Graph colouring options can be accessed in two ways. Both options provide quick access to the Graph colouring tab of the advanced settings dialog. The following describes the methods of access:

- Via the Menu bar
  - Click on the "Format" in the menu bar
  - Choose the "Advanced Settings" option see figure 7.1.1 - 1
  - Look for the "Graph Colouring" tab and click on it as shown in figure 7.1 - 1

Figure 7.1.1 - 1: Accessing the advanced settings menu

- By Clicking on the Graph Colouring Button on the Status Bar
  - Look for the "Graph Colouring" tab and click on it as shown in figure 7.1 - 1

Figure 7.1.1 - 2: The Graph Colouring Button on the Status Bar

7.2 Drawing / Dragging Graph options

An Osprey network can be in one of two modes at any given time:

- Drawing: An Osprey network is in drawing mode, when the graph is stationary, and no nodes are currently being moved around the screen.
- Dragging: An Osprey network is in dragging mode whenever a single node, or a group of nodes are being dragged about the network display area.

When in either of these modes, several preferences can be set that determine what Osprey will display to the screen. When in drawing mode, users have the option of displaying any combination of Nodes, Labels, Edges, and Arrows. When in dragging mode, users have the option of displaying Nodes, Edges, and Labels. In addition to this, when in dragging mode, the user has the ability to determine whether or not these options will be reflected on all nodes in the graph, or only on nodes directly connected to the set that is being dragged, by clicking the always option. By clicking the checkbox that corresponds to any of these settings Osprey will switch between displaying or not displaying the given option.

7.2.1 Accessing Drawing/Dragging graph options

Dragging and Drawing options can be accessed via two methods in Osprey:

- Status Bar Options
  - Click on the status bar button on the bottom of the screen
  - The drop-down menu displays "Draw" when the graph is stationary and "Drag" when the graph is being dragged.
  - When the drop-down menu says "Draw" the four checkboxes beside it show what is being displayed to the graph when it is stationary
  - When the drop-down menu says "Drag" the four checkboxes beside it show what is being displayed to the graph when it is being dragged
  - Turn any of these on or off by clicking the appropriate checkbox, see figure 7.2.1 - 1

Figure 7.2.1 - 1: The Drawing/Dragging options area in the Osprey Status Bar

- Via the Menu bar
  - Click on "Format" in the Menu bar
  - Click on "Advanced Settings"
  - Click on "Drawing Graph" as shown in Figure 7.2.1 - 3 or "Dragging Graph" as shown in Figure 7.2.1 - 4
  - Turn any of these on or off by clicking the appropriate checkbox

Figure 7.2.1 - 2: The advanced settings option in the "Format"

Figure 7.2.1 - 3: The Drawing Graph tab of the Advanced Settings Dialog

Figure 7.2.1 - 4: The Dragging Graph tab of the Advanced Settings Dialog

7.3 Node Options

Nodes can be coloured by their biological process as defined by standardized Gene Ontology (GO) annotations. Nodes that have been assigned more than one GO process are represented as multicolored pie charts. Osprey currently recognizes 29 biological processes derived from the categories maintained by the GO Consortium. Users have the option of displaying nodes by these colours, or by their own set of user defined colours. By choosing GO Process, nodes will be coloured based on the appropriate GO annotation category.

Note: Each of these options will continue to apply to all new nodes that get added to the screen after the option has changed.

7.3.1 Choosing Method of Colouring Nodes

There are two methods of switching the setting that Osprey uses to colour nodes in the Network display area. To view a listing of colours used when in Go Process colouring mode, view the GO Process colour index ( see section 4.6 Colour Indices ). The following describes these methods of access:

- Via the Status Bar
  - The status bar button will either say "Go Process" or "User Defined" reflecting the chosen mode of colouring
  - To change it click on the button and pick the method of choice, see figure 7.3.1 - 1
  - The change will be reflected immediately on the graph

Figure 7.3.1 - 1: How to switch between colouring by GO Process or user defined via the Status Bar

- Via the Menu Bar
  - Click on the "Format" menu in the menu bar
  - Click on "Advanced Settings" option, see figure 7.2.1 - 2
  - Click on the Colour Nodes/Edges by tab to access the node colouring options, see figure 7.2.1 - 3

Figure 7.2.1 - 2: The advanced settings option in the "Format"

Figure 7.2.1 - 3: The Colour Nodes By Option in the Advanced Settings Menu

7.3.2 User Defined Node Colours

User defined colours do not reflect any annotation stored in Osprey or The GRID. This option is used to manually colour nodes at the users discretion. Osprey is in User Defined mode whenever GO Process colours are not being used to colour nodes.

Note: To view nodes in User Defined Colours, user defined mode has to be selected as described in section 7.3.1 Choosing Method of Colouring Nodes.

When in user defined mode, node colours can be changed in the following two ways:

- Toolbar Node Colour Button
  - Select all the nodes whose colours you want changed
  - Click on the Node Colour selection button on the Toolbar as shown in figure 7.3.2 - 1
  - From the resulting node colour choosing window, you can now choose the colour to reflect on the nodes. For more information on the colour choosing window, see section 7.3.3 Colour Choosing Window. User defined node colours will immediately be reflected on the selected nodes in the Network Display Area.

Figure 7.3.2 - 1: The Node Colour Selection button on the Osprey Toolbar

- Via the Menu bar
  - Select all the nodes whose colours you want changed
  - Click on the "Format" menu from the Menu bar
  - Click on the "Nodes" submenu
  - Choose the Colour option to change the User Defined Node Colours, see figure 7.3.2 - 2
  - From the resulting node colour choosing window, you can now choose the colour to reflect on the User Defined nodes. For more information on the colour choosing window, see section 7.3.3 Colour Choosing Window. User defined node colours will immediately be reflected in the selected nodes in the Network Display Area.

Figure 7.3.2 - 2: The Node Colour Option of the Format Menu on the Menu bar

7.3.3 Colour Choosing Window

Whenever you change colours of anything in Osprey, you are presented with the Osprey colour chooser. This colour chooser has several key areas that allow for the most flexibility when customizing colour settings. These sections are as follows:

- Swatches Tab
- HSB Tab
- RGB Tab

7.3.3.1 Swatches tab

The "Swatches" tab has a standard set basic colours that can be picked as the colour of choice. To pick a colour from the "Swatches" tab simply click on it, the colour will appear at the bottom of the screen, then click "OK" to actually apply the colour change

Figure 7.3.3.1 - 1: The Osprey Colour Chooser with the Swatches Tab Selected

7.3.3.2 HSB tab

Hue, saturation, and brightness are aspects of color in the red, green, and blue (RGB) scheme. These terms are most often used in reference to the color of each pixel in a cathode ray tube (CRT) display. All possible colors can be specified according to hue, saturation, and brightness (also called brilliance), just as colors can be represented in terms of the R, G, and B components. [http://whatis.techtarget.com/definition/0,,sid9_gci212262,00.html]

To pick a colour from this tab you must first move the vertical chooser to determine the desired Colour hue. After the hue is chosen, you can click on the the colour window to change the Saturation and Brightness of the colour. When the desired colour is chosen click on "OK" to apply the colour to the Osprey Network Display Area.

Figure 7.3.3.2 - 1: The Osprey HSB Tab of the Colour Chooser

7.3.3.3 RGB tab

RGB (red, green, and blue) refers to a system for representing the colors to be used on a computer display. Red, green, and blue can be combined in various proportions to obtain any color in the visible spectrum. Levels of R, G, and B can each range from 0 to 100 percent of full intensity. Each level is represented by the range of decimal numbers from 0 to 255 (256 levels for each color). [http://whatis.techtarget.com/definition/0,,sid9_gci212900,00.html]

The RGB tab of the Colour chooser allows for greater flexibility when selecting the perfect colour for displaying in Osprey.

Figure 7.3.3.2 - 1: The Osprey RGB Tab of the Colour Chooser

7.3.4 Node Size

In addition to changing colours of nodes, Osprey also provides the ability to manipulate the physical size of nodes on the screen. To accomplish this, we have two major methods of accessing the node size:

- Node Size Selection Box
  - Select all nodes whose size needs to be changed
  - Select the desired size from the node size selection box, see figure 7.3.4 - 1
  - Node size changes are reflected immediately on the Network Display Area

Figure 7.3.4 - 1: The Node Size Selection Box

- Node Size Configuration Dialog
  - Select all nodes whose size needs to be changed
  - Click on the "Format" menu in the Menu bar
  - Click on the "Nodes" submenu
  - Click on "Size", see figure 7.3.4 - 2
  - Use the node size slider to increase or decrease the size of a node, see figure 7.3.4 - 3
  - Node size changes are reflected immediately on the Network Display Area

Figure 7.3.4 - 2: The Nodes submenu in the Format menu

Figure 7.3.4 -3: The Node size slider

7.4 Edge Options

Similar to nodes, edges also have the ability to be coloured by annotation. Osprey provides three major methods of colouring edges. They are as follows:

- User Defined: This option allows for individual customization of edge colouring. When set to user defined, Osprey will display colours chosen by the user to represent the individual edges. In this mode, edges cannot be segmented into multiply coloured pieces.
- Experimental System: When activated, edges in Osprey will be coloured according to the experimental systems that are reflected by the interaction. Edges can be segmented into multiple pieces with this method, where each segment represents a different experimental system.
- Sources: When this option is activated, edges in Osprey will be coloured according to the sources that reported the interaction. Edges can be segmented into multiple pieces with this method where each segment represents a different source from which we have obtained this interaction.

Note: Each of these options will continue to apply to all new edges that get added to the screen after the option has changed.

7.4.1 Choosing Method of Colouring Edges

There are two methods of switching the edge colouring setting that Osprey uses to colour edges in the Network Display Area. To view a listing of colours used when in either experimental system mode or source mode, view the respective colour index ( see section 4.6 Colour Indices ). The following describes these methods of access:

- Via the Status Bar
  - The status bar button will either say "Exp System", "Source", or "User Defined" reflecting the chosen mode of colouring, see figure 7.4.1 - 1
  - To change it click on the button and pick the method of choice
  - The change will be reflected immediately on the graph

Figure 7.4.1 - 1: The Edge Colouring option on the Status Bar

- Via the Menu Bar
  - Click on the "Format" overhead menu
  - Click on "Advanced Settings" option, see figure 7.4.1 - 2
  - Click on the Colour Nodes/Edges by tab to access the edge colouring options, see figure 7.4.1 - 3

Figure 7.4.1 - 2: The advanced settings option in the "Format"

Figure 7.4.1 - 3: The Colour Edges By Option in the Advanced Settings Menu

7.4.2 User Defined Edge Colours

To view User Defined Coloured Edges the user defined mode has to be chosen for edges as described in section 7.4.1 Choosing Method of Colouring Edges . There are two ways to manipulate user defined colours. It can be done in one of the following ways:

- Toolbar Edge Colour Button
  - Select all the edges whose colours you want changed
  - Click on the edge Colour selection button on the Toolbar as shown in figure 7.3.2 - 1
  - From the resulting edge colour choosing window, you can now choose the colour to reflect on the User Defined edges. For more information on the colour choosing window, see section 7.3.3 Colour Choosing Window. User defined edge colours will immediately be reflected in the selected edges in the Network Display Area.

Figure 7.4.2 - 1: The Edge Colour Selection button on the Osprey Toolbar

- Via the Menu bar
  - Select all the edges whose colours you want changed
  - Click on the "Format" menu from the Menu bar
  - Click on the "edges" submenu
  - Choose the Colour option to change the User Defined Edge Colours, see figure 7.4.2 - 2
  - From the resulting edge colour choosing window, you can now choose the colour to reflect on the User Defined edges. For more information on the colour choosing window, see section 7.3.3 Colour Choosing Window. User defined edge colours will immediately be reflected in the selected edges in the Network Display Area.

Figure 7.4.2 - 2: The Edge Colour Option of the Format Menu on the Menu bar

7.4.3 Edge Size

In addition to changing colours of edges, Osprey also provides the ability to manipulate the physical size of edges on the screen. To accomplish this, we have two major methods of accessing the edge size:

- Edge Size Selection Box
  - Select all edges whose size needs to be changed
  - Select the desired size from the edge size selection box, see figure 7.4.3 - 1
  - Edge size changes are reflected immediately on the Network Display Area

Figure 7.4.3 - 1: The Edge Size Selection Box

- Edge Size Configuration Dialog
  - Select all Edges whose size needs to be changed
  - Click on the "Format" menu in the Menu bar
  - Click on the "Edges" submenu
  - Click on "Size", see figure 7.4.3 - 2
  - Use the edge size slider to increase or decrease the size of a node, see figure 7.4.3 - 3
  - Edge size changes are reflected immediately on the Network Display Area

Figure 7.4.3 - 2: The Edges submenu in the Format menu

Figure 7.4.3 - 3: The Edge size slider

7.5 Arrow Head Options

Similar to nodes and edges, arrow heads also have the ability to be coloured. Osprey only allows for User Defined colouring of Arrow Heads, and as such provides no additional annotation data to the Arrows themselves. Users can manipulate the colour of the arrow heads in order to manipulate the current network.

Note: Each of these options will continue to apply to all new edges with arrow heads that get added to the screen after the option has changed.

7.5.1 User Defined Arrow Head Colour

There are two ways to manipulates the user defined arrow head colours. It can be done in one of the following ways:

- Toolbar Arrow Head Colour Button
  - Select all the edges whose arrow head colours you want changed
  - Click on the arrow head colour selection button on the Toolbar as shown in figure 7.5.1 - 1
  - From the resulting colour choosing window, you can now choose the colour to reflect on the User Defined arrow heads. For more information on the colour choosing window, see section 7.3.3 Colour Choosing Window. User defined arrow head colours will immediately be reflected in the selected edges in the Network Display Area.

Figure 7.5.1 - 1: The Colour setting of the Arrows submenu

- Via the Menu bar

- Select all the edges whose arrow head colours you want changed
- Click on the "Format" menu from the Menu bar
- Click on the "arrows" submenu
- Choose the Colour option to change the User Defined arrow head colours, see figure 7.4.2 - 2
- From the resulting arrow head colour choosing window, you can now choose the colour to reflect on the User Defined arrow heads. For more information on the colour choosing window, see section 7.3.3 Colour Choosing Window. User defined arrow head colours will immediately be reflected in the selected edges in the Network Display Area.

Figure 7.5.1 - 2: The arrow head Colour Option of the Format Menu on the Menu bar

7.5.2 Arrow Head Size

In addition to changing colours of arrow heads, Osprey also provides the ability to manipulate the physical size of an arrow head in proportion to the size of the edge it resides on. To accomplish this, we have two major methods of accessing the arrow head size:

Note: Arrow Heads will change size proportionally to edge sizes

- Arrow Head Size Selection Box
  - Select all edges whose arrow head size needs to be changed
  - Select the desired size from the arrow head size selection box, see figure 7.5.2 - 1
  - Arrow head size changes are reflected immediately on the Network Display Area

Figure 7.5.2 - 1: The Arrow Head Size Selection Box

- Edge Size Configuration Dialog
  - Select all Edges whose arrow head size needs to be changed
  - Click on the "Format" menu in the Menu bar
  - Click on the "Arrows" submenu
  - Click on "Size", see figure 7.5.2 - 2
  - Use the arrow head size slider to increase or decrease the size of an arrow head, see figure 7.5.2 - 3
  - Arrow head size changes are reflected immediately on the Network Display Area

Figure 7.5.2 - 2: The Arrows submenu in the Format menu

Figure 7.5.2 - 3: The Arrow Head size slider

7.6 Label Options

In addition to manipulating the size of nodes and edges in Osprey, we also provide the ability to manipulate the text that comprises the label ( screen name ) of a node. The following lists the major label options that are provided:

- Manipulating Label Font Size
- Manipulating Label Font
- Manipulating Label Style
- Manipulating Label Colour

Each of these options are readily available via the Osprey toolbar, as well as via the Osprey Menu bar.

Note: Each of these options will continue to apply to all new labels that get added to the screen after the option has changed.

7.6.1 Label Size

Osprey offers two methods for manipulating the size of a label. Before attempting to change the size of a label, ensure that you have at least one node selected in the Network Display Area. The following describes the two major methods of accessing the label size:

- Label Size Selection Box
  - Select all labels whose size is to be changed.
  - Select the desired size in the Osprey size selection box, see figure 7.6.1 - 1
  - Changes to font label size are immediately reflected on the Network displayed in the Network Display Area

Figure 7.6.1 - 1: The Osprey Label Size Selection Box

- Via the Menu bar
  - Select all the nodes whose label size you want changed
  - Click on the "Format" menu from the Menu bar
  - Click on the "Text" submenu
  - Choose the font option to change the label size, see figure 7.6.1 - 2.
  - From the resulting font options dialog, you have the ability to manipulate the size as well as most other label options described in this section, see figure 7.6.1 - 3..

Figure 7.6.1 - 2: The Text submenu in the Format menu

Figure 7.6.1 - 3: The font options dialog

7.6.2 Label Font

Osprey offers two methods for manipulating the font of a label. Before attempting to change the font of a label, ensure that you have at least one node selected in the Network Display Area. The following describes the two major methods of accessing the label font:

- Label Font Selection Box
  - Select all labels whose font is to be changed.
  - Select the desired font in the Osprey font selection box, see figure 7.6.2 - 1
  - Changes to label font are immediately reflected on the Network displayed in the Network Display Area

Figure 7.6.2 - 1: The Osprey Label Font Selection Box

- Via the Menu bar
  - Select all the nodes whose label font you want changed
  - Click on the "Format" menu from the Menu bar
  - Click on the "Text" submenu
  - Choose the font option to change the label font, see figure 7.6.1 - 2.
  - From the resulting font options dialog, you have the ability to manipulate the font as well as most other label options described in this section, see figure 7.6.2 - 2..

Figure 7.6.2 - 2: The Font Options Dialog

7.6.3 Label Style

Osprey offers two methods for manipulating the style of a label. Before attempting to change the style of a label, ensure that you have at least one node selected in the Network Display Area. The following describes the two major methods of accessing the label style:

- Label Style Selection Buttons
  - Select all labels whose style is to be changed.
  - Click the desired style button ( Bold, Italic, or Both ) in the Osprey toolbar, see figure 7.6.3 - 1
  - Changes to label style are immediately reflected on the Network displayed in the Network Display Area

Figure 7.6.3 - 1: The Osprey Label Style Selection Buttons

- Via the Menu bar
  - Select all the nodes whose label style you want changed
  - Click on the "Format" menu from the Menu bar
  - Click on the "Text" submenu
  - Choose the "Font" option to change the label style, see figure 7.6.1 - 2.
  - From the resulting font options dialog, you have the ability to manipulate the font style as well as most other label options described in this section, see figure 7.6.3 - 2..

Figure 7.6.3 - 2: The Font Options Dialog

7.6.4 Label Colour

Osprey offers two methods for manipulating the colour of the text in a label. Before attempting to change the colour of a label, ensure that you have at least one node selected in the Network Display Area. The following describes the two major methods of accessing the label colour:

- Label Colour Selection Box
  - Select all labels whose font colour is to be changed.
  - Select the desired color in the from the resulting colour choosing window, see section 7.3.3 Colour Choosing Window
  - Changes to label colour are immediately reflected on the Network displayed in the Network Display Area

- Via the Menu bar
  - Select all the nodes whose label colour you want changed
  - Click on the "Format" menu from the Menu bar
  - Click on the "Text" submenu
  - Choose the "Colour" option to change the label colour, see figure 7.6.4 - 2.
  - From the resulting colour choosing window, see section 7.3.3 Colour Choosing Window, you have the ability to manipulate the colour.

Figure 7.6.4 - 2: The Text Submenu for changing Colour

7.6.5 Hiding Labels

In Osprey, you have the ability to manipulate the visibility of individual node labels. You can turn the label of any node on and off to help make figures and images. This can be accomplished in the following way:

- Via the Menu bar
  - Select all the nodes whose label you want to Hide or Show
  - Click on the "Format" menu from the Menu bar
  - Click on the "Text" submenu
  - Choose "Show" or "Hide" depending on whether you want to show or hide the selected labels, see figure 7.6.3 - 1

Figure 7.6.5 - 1: The Text submenu with the Show and Hide options highlighted

7.7 Background Colour

In addition to changing colours and sizes of individual objects on the Network Display Area, such as nodes, edges, and labels, Osprey also provides options for changing the entire background of the Network Display Area. This option is useful for creating networks that are more colourful and allow for more colours in highlighting specific features of a graph. For example, labels or nodes that are coloured white may be important in specific circumstances, but a background of white would make these invisible. Changing the background to black or blue, however, would make it a lot easier to visualize white colour objects.

7.7.1 Accessing Background Colour

The background colour can be changed using one of the following two methods:

- Via the Menu bar
  - Click on the "Format" menu from the Menu bar
  - Click on the "Background Colour" option
  - Simply choose the colour you want for the background using the Osprey Colour Chooser, see section 7.3.3 Colour Choosing Window

Figure 7.7.1 - 1: The Background Colour option of the Format menu

- Via the Advanced Settings Dialog
  - Click on the "Format" menu from the Menu bar
  - Click on the "Advanced Settings" option, see figure 7.7.1 - 2
  - Click on the "Background" tab, see figure 7.7.1 - 3
  - Click on the "Change Default Background" button, see figure 7.7.1 - 4, and select the new background colour from the Osprey Colour Chooser, see section 7.3.3 Colour Choosing Window

Figure 7.7.1 - 2: The Advanced Settings option of the Format menu

Figure 7.7.1 - 3: Advanced Settings Dialog

Figure 7.7.1 - 4: The Change Default Background Button in Advanced Settings

7.8 Saving Preferences

Osprey provides the ability to save network preferences so that they are maintained each time the application is launched. With this, users can fully customize the look and feel of their networks, including all settings described in section 7. Osprey Preferences and Customization, and ensure that each time they launch Osprey, these settings will be maintained.

7.8.1 Saving settings

Osprey provides two different options for saving settings. These options allow the user to customize certain aspects of the application so that they may be maintained with each initialization of the application. The types of settings that can be saved within Osprey are:

- Advanced Settings
- Colour Settings

7.8.1.1 Saving Advanced Settings

Advanced Settings include all the settings in the Advanced Settings Menu as well as all user defined node, edge, label and arrow sizes and colours. Follow these steps to save the advanced settings:

- Click on "File" from the menu bar
- Click on the "Save Settings" submenu
- Click on save "Advanced Settings" option

Note: This option will take all of your settings, described above, and will initialize Osprey with these settings each time the application is run.

Figure 7.8.1.1 - 1: The advanced settings save option

7.8.1.2 Saving Colour Settings

Colour settings are all the colour index settings in the Go Process index, Experimental Colour index and Source index as discussed in section 7.3.2 User Defined Node Colours and section 7.4.2 User Defined Edge Colours. These are the colour specific settings for exactly how to colour each and every annotation that is displayed on an edge or a node in Osprey. Follow these steps to save the colour settings:

- Click on the "File" from the menu bar
- Click on the "Save Settings" submenu
- Click on save "Colour Settings"

Note: 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 7.8.1.2 - 1: The Colour Settings save option

7.9 Proxy Settings

In order to get Osprey to connect to the internet through a proxy server you must do the following:

1.) Open the "Advanced Settings" window by going to the "Format" -> "Advanced Settings" menu, see figure 7.9 -1.
2.) Check the box "Web Proxy (HTTP)" to indicate if you want to us a proxy or not.
3.) Fill in the Proxy URL, Port, and User Name and Password if they are required.
4.) Press "Apply Now" to apply the changes.

Figure 7.9 - 1: Proxy Settings

7.10 Changing Databases

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.

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.

There are currently 3 ways in which you can change the database in which Osprey will connect to for interaction and annotaion information:

1.) On Start-up

New to version 1.2.0 is the ability to change the database during the inialization stage of Osprey. If it is the first time that you have run Osprey you'll be promted with the screen shown in figure 7-10.1. Here you'll have the ability to set the following:

a.) Select the database you would like Osprey to connect to.
b.) Make the selection the default database in the future.
c.) Decide whether or not you want this screen to show up the next time you load Osprey.

Figure 7.10 - 1: Database Setting on Osprey Start-up

NOTE: If Osprey can not find an active network connection at start-up this screen will not appear.

2.) Using the "Change Database" option under the "Database" menu item

Figure 7.10 - 2: Changing database from "Database" menu item

3.) Inside the "Database Settings" section of the "Advanced Settings" window.

From the "Advanced Settings" window, see section 7.1.1 for details on how to access, select the "Database Settings" option and figure 7-10-3 is what you'll be
preseneted with. In this window you have the option of simple changing the database or setting the selected database as the default. If you where to select the "Change Database" option you would be presented with the window shown in figure 7-10-4 where you'll be asked to select the database you would like to connect with. Note: if you are in offline mode then any changes you make to the database settings will not take affect until you restore the network connection.

Figure 7.10 - 3: Changing database from "Advanced Settings"
Figure 7.10 - 4: Changing database options

Note: 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.

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 7.10-5, and 7.10-6 for examples.
Figure 7.10-5: Osprey currently connected to the "Yeast GRID" which contains the yeast database
Figure 7.10-6: Osprey currently connected to the "Fly GRID" which contains the fly database

7.11 Memory Settings

Due to the increasing size of networks being published, Osprey may need to have its memory settings changed to be able to handle the thousands of objects being manipulated. Some signs that may point to a memory problem include:
1.) Osprey hangs while trying to open, save or export a file.
2.) Osprey takes and extremely long time to draw the network.
By default, as of Osprey 1.2.0, 128Mb of memory has been allocated to the java virtual machine that powers Osprey. This is generally enough memory to handle networks containing ~5000 nodes and ~10,000 edges. Once your network start getting larger than this you'll notice a hit in performance while manipulating the network.
There are two ways in which you can increase the amount of memory to Osprey:
1.) For users that have the currently release of Java installed you can launch Opsrey via the command line as follows:
java -jar -Xmx256m Osprey.jar
Osprey.jar will be located in the folder in which you installed Osprey. The -Xmx256m sets the maximum heap size for Java, in this case it is set to 256MB. Adjust this number to the appropriate size based on the amount of memory you currently have available. In practice you should never increase this number more than half of your total memory. For example if you have 1024MB of memory than you should never go larger than 512MB. This technique will work for all the operating systems that Osprey has been tested for and have a working/updated version of Java. Osprey 1.2.0 was compiled using the 1.4.2_03 compiler.
2.) Windows users Only! To increase the memory to Osprey using Windows, find the file "osprey 1.2.0.lax" located in the default location that Osprey was installed. Open the file and find the line starting with "lax.nl.java.option.java.heap.size.max=". The number that follows indicates the memory allocated to the Java Virtual machine in bits. So, if you want to increase the memory to 256MB ( 268435456bits ) you would replace the line with "lax.nl.java.option.java.heap.size.max=268435456" and save the file.
NOTE: Mac OSX users can use the command line option above because java should come pre-installed with the operating system. If you do not have java installed simple run your software update and download the latest java.

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

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