Colours can be used to improve the clarity or emphasise the role or grouping of the various network constituents - the choice is up to the user.
NetBuilder has a menu option, Symbols:Active colours. If this option is set (which it is by default), the View of the Nucleus (Simulation mode) looks quite different from the View of the Genome (Design mode): in the View of the Nucleus, 'active' nodes and their dependent links are coloured as in the View of the Genome, but their lines are slightly thicker, whereas 'inactive' nodes and links are grey, and have thinner lines than the active constituents.
Colours can be changed in two ways: via the properties option in the menu that pops up after right clicking a component, and via the quicker (and presently safer) Symbol parameters toolbar shortcut. Selecting the symbol, or symbols that you want to give a particular colour, and press the Symbol colour button to apply the currently set colour, and the Palette button to choose and apply another colour.
In the Simulation mode, links that are connected to the output port of a symbol will automatically assume the same colour as the symbol. To achieve the same in the Design mode, press the Update colours button on the Symbol parameters toolbar.
Apply a colour scheme as in the picture below to your network. Furthermore, name the three components (red, green, and orange) TF1, TF2, and TF3 (by selecting them, pressing the Name button on the Symbol parameter toolbar, and changing their default names to the ones above by double clicking and editing the name labels).
The design is now ready, and its state in the different cells can be displayed as Views of the Nucleus.