The Rule page describes the interactions between the agents in the model. Additionally, this page describes any state changes that occur to those agents.

Panel 1 - Rule description and actions

Users can add a title by clicking on the blue text and then clicking "Save". A rich text description of the rule can also be added. "Copy" allows users to copy a rule into another cBook or make a copy of it in the current cBook. From the Actions menu, users can create a new rule from the RHS (right hand side) or LHS (left hand side) of the diagram, and delete the rule.

Panel 2 - Rule Creation (edit mode)

Dragging agents into the rule editor will open a live look-up menu where users can pick agents, relevant sites and create agents. States can be added by clicking on the State button when a site is selected, or dragging the button onto a site . Bonds can be added by dragging the Bond button onto a site or clicking on the button when site is selected.  Different types of bonds can be added by clicking on the bond. Users can zoom in and out on the rule, and can edit the rule in full screen as well.

Rate constants use elementary chemical kinetics and can be added in scientific notation.  Rules can be made reversible by adding a "Backward rate constant". Users can change the units of rate constants by clicking "Change Forward Units" or "Change Backward Units". In viewing mode, hovering over the two center arrows will reveal the rate constants of the rule.

Kappa can be edited directly in the "Kappa String". Users can save their changes to the rule or cancel out. In addition, users can navigate to the contact map and the influence map via their appropriate tabs.

Panel 3 - Annotations

For more on Annotations, click here.

Panel 4 - Related Agents and Models

This displays links to the agent(s) involved in the rule and the model(s) that the rule is in.