Observable Properties Pane

The Observables are specified and edited using mouse right click in the bottom Object Properites pane. Only annotation can be typed in.

• Each Observable consists of one or more Species Patters. Observable selects species that match at least one of the species patterns (not both).
• Each species pattern defines common features of species. It consists of one or more of molecules that compose species. Molecules may or may not be explicitely connected, but must be present in every species selected by this species pattern.
• Sites that have possible multiple states have yellow sign above site shape. Each molecule within species pattern may have some sites being undefined. If site does not have defined states (if states are possible) and its binding is not important, it is shown in white. Sites may have defined binding - they can be declared to be explicitly bound to another site, declared unbound or declared bound to "some" (unspecified) site - then the site is shown in green with bond (if exists) shown in solid color.
• Observable below describes the total phosphorylation of all EGFR molecules. The first species pattern selects all species that have Y1068 being phosphorylated, the second - all species that have Y1148 phosphorylated.

Observable specification

• Right click mouse on the shape to select the first molecule for the first species pattern.
  
  
• Right click on molecular site or state will allow editing. Right click next to molecule will add another molecule.
  
  
• To add another species patter, right click below the first.
  
  
• Similarly to the first species pattern, clicking on shape will allow selection of molecule:
  
  
• The second species patter is edited through right click on site and state.