Figure 2

Formalisms with visual representation Toy examples of the formalisms with visual representation. a) Boolean network: genes are represented by nodes (a, b, c, d) and the arrows represent activation and repression; b) Bayesian network: the value of the output nodes (genes c, d, e) are given by a probability function that depends on the value of the input nodes (genes a and b); c) Petri net: places represent substances (a, b, c), transitions represent reactions (p, q) and the arrows represent consumption and production; d) Agent-based model: two types of agents, representing two different kinds of cells (or two kinds of molecules) can move freely and interact within the containing space; e) Interacting state machine: systems are represented by their state (a, b), where each state may contain one or more internal sub-states (b, d, e), arrows represent the transition between different states of the system; f) Rule-based model (represented by a contact map): agents represent proteins (P, Q, R, S), which may contain different binding sites (a to f ), the connections represent the rules for possible interactions (such as phosphorylation); g) Cellular automata: a grid where the value of each element can represent different kinds of cells (or molecules), that can change by interaction with their immediate neighbors.