Figure 1.

A schematic of a generic GRN/pathway paradigm

A standard conceptual formalism with which to understand biological outcomes is that of a “pathway” including protein interaction and gene-regulatory networks. It describes the relationships between nodes and the strength and direction of their interaction (repressive, dashed lines, or activating, solid lines). Loops and self-loops are common. The dynamics of the system as a whole (its “behavior”) are taken to be accurately described by the topology of the connections and parameters in this circumscribed way—in other words, it draws a causal boundary around a given set of molecular players and focuses attention on their interactions. It provides a fundamentally mechanistic, local, single-level organization perspective. Image courtesy of Jeremy Guay.