# Graphical Modeling

The graphical rule based modeling used in BioNetGen follows a simple representational scheme where each partition of a graph denotes a single molecule. Partitions are indicated by boxes surrounding collections of one or more nodes. Within a partition, nodes denote components and edges represent bonds between components. Bonds that can form or break during signaling are the only ones that are explicitly drawn.

Node conventions include empty nodes as unbound components, half-filled nodes as components that may be bound or unbound and filled-nodes as components that are bound. Node labels give the name of the component, and, if the component is allowed to have multiple states, state information as well.