Hierarchy-dependent instantiation of rules. Due to population-based aggregation of species, the propensity (firing rate) of a rule instantiation is not only determined by the actual rate of a schematic rule (here the amount of green triangles and blue diamonds) but it is also context dependent, i.e. it is proportional to the amount of enclosing species. Therefore, enumeration of rule instantiations requires to calculate the propensity p dependent on the whole hierarchy above the matched reactant species. For example, the propensity of the rightmost matching is proportional to 2·2·1·2 = 8, where the first two factors correspond to the amount of triangles and diamonds, the third describes the single enclosing rectangle, and the last factor corresponds to the amount of the outermost enclosing species (light blue with round corners).
Maus et al. BMC Systems Biology 2011 5:166 doi:10.1186/1752-0509-5-166