The Workspace is the main window of Cell Illustrator. It can function in two modes: the original CI mode and the Gene Net mode. The mode of working can be switched by choosing the menu command View | Gene Net Mode. Depending upon which mode is selected the program menus and toolbars are changed. This manual describes the user interface available in the Gene Net mode only.
The Menu Bar located at the top provides a set of commands for building and manipulating a model. Frequently used commands can be also executed by pushing a button on one of the toolbars on the sides of Workspace. Menu items and toolbar buttons corresponding to operations that cannot be performed at that moment are disabled (grayed out).
In the Workspace, multiple model files can be opened simultaneously for viewing and editing. A model file is displayed in a canvas window. The canvas window is the main view of the model and allows the model to be edited.
In Cell Illustrator, the user can open several property dialogs. The contents of these dialogs reflect:
- user preferences (applicable to all models),
- properties of the model in the active canvas window
The list of property dialogs in Gene Net mode is as follows:
Dialog name |
Purpose |
Displays lists of model elements and values of their main properties. |
|
Allows the viewing and the setting of the properties of a selected element. |
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Allows for viewing/editing the list of external references |
|
Allows the setting of application-wide usage options. |
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Displays the expression plot for the selected edge |
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Displays the partial residual plot for the selected edge |
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Facilitates an automated layout of model elements on the canvas |
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Allows to view, define and combine the subnets in the active canvas. |
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Searches for specified elements in the canvas. |
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Searches for pathways in the selected network |
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Searches for a list of genes in the selected network |
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Searches for publications and links for the selected genes |