Figure 3.

Graphical representation of reaction rules and reaction networks. (A) Shown here is a collapsed VCell reaction diagram of a rule-based model for Ran transport across nuclear membrane. Ran can bind cargo molecule C in both nucleus (rule 1) and cytoplasm (2). In nucleus, Ran can bind RCC1 (3), whereas in cytoplasm, cargo protein may undergo phosphorylation on all their phosphosites (4, 5, 6). Ran can undergo transport across the nuclear membrane (7). The full mechanisms (such as what should be bound to Ran in rule 7) are hidden in this view, but can be seen when the user clicks on a reaction rule node. (B) The reaction network generated within VCell from this set of rules contains 36 species and 98 reactions. To see this figure in color, go online.