The Workspace is the main window of Cell Illustrator. 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 the 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 and a simulation run to be watched. You can open several canvas windows to view different parts of the model. However, only the canvas window active at the time of starting simulation remains open when the simulation runs.
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, or
- properties of a selected model in the active canvas window.
The list of property dialogs follows:
Dialog name |
Purpose |
Displays lists of model elements and values of their main properties. |
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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 for the selected entity |
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Shows the position of the canvas window relative to the whole model. |
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Allows the setting of application-wide usage options for CI16. |
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Allows the setting of application-wide view options. |
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Allows the selection of variables to be watched in a chart window when simulation is running. |
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Displays simulation parameters. |
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Displays the list of simulation logs |
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Facilitates the definition of new units for the selected model |
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Allows the addition of model items from the set of predefined biological elements |
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Facilitates an automated layout of model elements on the 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 publications and links for the selected genes |