Figure 4. Example of a Boolean network produced by toyLIFE rules.

The inputs of the truth table (possible initial states) are all combinations of states of three toyGenes. Whenever a toyGene is active, the protein it codes for is present. The main panel schematically represents all relevant interactions between molecules: in this case the toyPolymerase may bind to the promoter regions of toyGenes 1 and 2 (+ signs), and toyProtein 1 inhibits the expression of toyGene 2 (− signs). The simultaneous presence of toyProteins 1 and 3 leads to toyDimer 1–3, and the simultaneous presence of toyProteins 1 and 2 to toyDimer 1–2. Both toyDimers inhibit the expression of toyGene 2 and activate the expression of toyGene 3. The construction of the Boolean functions codified in the truth table is straightforward given the interactions conditional on presence or absence of each toyProtein. The truth table maps every possible initial state (g_i) to its corresponding regulatory output (). When the truth table is represented as a directed graph (summarising the dynamics of the system from all possible initial conditions) it is seen that there are two attractors for the dynamics: (1, 0, 1), whose basin of attraction has size 7, and (1, 0, 0), whose basin of attraction has size 1. (Note that the order of toyGenes in a genome is irrelevant, and only responds to aesthetic reasons.)