NetBuilder has a menu bar, a horizontal toolbars below the menu bar (Main and Edit), two vertical toolbars, one to the left of the main window (Design), and one to the right (Simulation), and another two below the main window (Draw and Symbol Parameters). All commands that are available on the toolbars can also be issued via the menu bar, but some menu commands have no toolbar representation. Open documents, which contain the 'canvas', are visible in the main window.
When the cursor hovers over a toolbar button, the general status bar in the main displays the function of the button, and when the cursor hovers over a symbol in the open document, the document status bar displays information about the symbol.
The Main toolbar contains buttons for the standard commands (New, Open, Save, Cut, Copy, Paste, Print), selection and view commands (Select, Pan, Zoom, Set to default zoom, Zoom to fit, Zoom to selection, Show Ports), and buttons for alignment, nudging, and rotation of objects. Some additional commands (Structure:Bring to front, Structure:Send to back, etc. are found under the Edit menu.
The Draw toolbar has buttons for adding text and general drawing to the document (Text, Line, Polygon, Rectangle, Ellipse). Symbols created using these commands will not have any functionality in the network).
The Design toolbar has buttons for adding and handling the functional network objects. The topmost button (Design) is disabled when NetBuilder is started up. The names of the other, enabled buttons are (from top to bottom): Component, Gene, Function, Simple link, Direceted link 1, Direceted link 2, Negated link, Cell, Receptor, and Contacts (disabled).
The Symbol Parameters toolbar contains the following buttons: Symbol colour, Palette, Update colors, Name, Type, Caption, and Parameter values. Most of these buttons are disabled at this stage.
The topmost button on Simulation toolbar, Simulate, is the only button enabled at this stage. The buttons underneath it are, from the top to the bottom: Probe, Monitor, Programmed simulation, Record, Set, Reset, Toggle, Timer, Go, and Stop.
The buttons on the Design, Symbol Parameters, and Simulation toolbars, and the Show ports button on the View toolbar, are unique to NetBuilder, and their function will be explained on the next pages.