Simulation of the TOL logicome in the presence or absence of m-xylene. Piecewise-linear differential equations describing the regulatory and metabolic events of the network were implemented in GNA software and the behavior of the TOL simulated in response to m-xylene. (a) Non-inducing conditions. The state transition graph resulting from the simulation is shown to the left with the shortest path between defined states indicated in color. The plots to the right show the temporal sequence of qualitative states for the two regulators (XylR and XylS) and the two pathways (upper and meta) in the selected path of the transition graph. (b) Induced conditions. The transition graph is shown to the left while the temporal sequence of qualitative states is displayed to the right. As before, color states highlight the shortest path in the transition graph.
Silva-Rocha et al. BMC Systems Biology 2011 5:191 doi:10.1186/1752-0509-5-191