3                   Workspace - Main Window of CI

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

Element Lists

Displays lists of model elements and values of their main properties.

Element Settings

Allows the viewing and the setting of the properties of a selected element.

External References

Allows for viewing/editing the list of external references for the selected entity

Navigator

Shows the position of the canvas window relative to the whole model.

Preferences

Allows the setting of application-wide usage options for CI16.

View Settings

Allows the setting of application-wide view options.

Chart Settings

Allows the selection of variables to be watched in a chart window when simulation is running.

Simulation Settings

Displays simulation parameters.

Simulation History

Displays the list of simulation logs

Edit Units

Facilitates the definition of new units for the selected model

Biological Elements

Allows the addition of model items from the set of predefined biological elements

Graph Layout

Facilitates an automated layout of model elements on the canvas

Finder

Searches for specified elements in the canvas.

Pathway Search

Searches for pathways in the selected network

Gene Mining

Searches for publications and links for the selected genes