What is a Rule? 

A rule is essentially a reconfiguration of agents representing a chemical reaction. The left hand side describes the pattern of agents required to trigger the rule (the "before" situation) and the right hand side describes the reconfigured pattern of agents that results from the application of the rule (the "After" situation). If the rule is made reversible (by adding a reverse rate constant), the notions of "Before" and "After" become interchangeable, since the right hand side agent pattern is the trigger for the reverse rule (which is automatically created for you if you make the rule reversible). The weight of a rule in simulations and stories, depends upon its kinetic rate and the concentration of the matching pattern of agents required to trigger it. There are five different types of rules: creation, binding, breaking, modification, and deletion. All the five types are made by dragging agents into the Left Hand Side (LHS) of the editor, while generation rules are made by dragging the agent into the Right Hand Side (RHS) of the editor. Learn more about the Rule Page itself.

Rule Creation:

1. Name the rule by clicking on blue text in the title field, enter name and save. Rule names can use characters except "<" or ">".  If a name isn't added, a default name "Rule_1" will be given, the next default name will be "Rule_2" and so on.  
2. To begin editing or creating the rule, click "edit rule". Since editing different side of rules has different consequences, the side of the rule being edited is outlined in green. 
3. Add agents to the rule by dragging the agent icon onto either side. This will open a live lookup drop down menu of all the agents in the cBook. You can use this menu/editor to create new agents and/or add sites to existing agents.

Bonds and/or states can be added to the sites on the agents. Bonds can be added by dragging the bond button to the appropriate site and releasing. There are three different types of bonds:

• Site-Site bond: To make a bond between sites, release the bond onto the one site and drag it to the second site.
• Anybond: The site is bound to something, anything. To make this, drop the bond on the site and drag it anywhere (not over another site)
• Wildcard bond: This site may or may not be bound (usually used with sites with states). To create the bond, drop the bond on the site and drag it anywhere (not over another site)  on the editor then click on the bond again. (link to complex editing page). 

Next, states can be added by dragging the state icon onto the site being modified. New states can be introduced in rules, there is no consistency check though states can only be added to sites that have a state on the agent page. 

The rule can also be edited in full screen and the agents can be viewed in different magnifications by clicking on the "+" and " -" . Editing can also be done directly to the kappa in the editor. Rate constants use elementary chemical kinetics and  clicking on the “change forward (or backward) Units” opens a list of units. Hovering over the center arrows shows the rule’s units.  Additionally, rules are made reversible by adding reverse rate constants. Once edits are done, click "save" to exit edit model or "cancel" to cancel edits.

Maps (understanding rule's context in cBook):

Once edits/rule creation is done,  the syntactic contact, influence map will be generated by clicking on their respective tabs related rules and models. The contact map shows connection between agents in cBook or model. The Contact Map is a "Who binds whom" diagram that shows the interactions between agents, as well as providing a powerful way to navigate your cBooks.  The influence map can be used as a powerful tool to navigate the rules based on the relationships you define in the model. The Influence Map shows both inhibitory (red edge) and inducible (green) relationships between rules in the model. A user can navigate to rules (by hovering over a rule) and can also explore all the potential "random-walks" that the model can generate.

Actions on Rule:

There are three actions that can be taken on rules that can be accessed from the top panel:

1. Rules can be copied by clicking "Copy" from top panel of the page. You can choose which bookshelf, cBook and chapter you want to copy to.
   
2. Additionally, new rule from the LHS or RHS can be created in the same cBook, the action appears in the Actions menu.
   
3. Finally, deleting rules (from the Actions menu) checks for dependencies and ensures that the rule is not in any models.

Finally, to create a clearer, more transparent rule, a description can be added by clicking on "Click to add description"  this opens up a rich text editor. Additionally, annotations can be added to link to the literature that supports the rule.