Figure 1

Generation of a bipartite Boolean model from the rxncon network definition. (A) The network is defined as elemental reactions (red nodes); that produce (blue edges) or consume (purple edges) elemental states (blue nodes), and contingencies showing how states activate (green edges) or inhibit (red edges) reactions. The elemental reactions correspond to the edges in topological networks, and the contingencies are contextual constraints on the reactions. This simplified version of the high osmolarity glycerol (HOG) pathway contains two modules: The upstream phosphotransfer module (green box) is active when turgor is sufficient, keeping the downstream MAP kinase module (yellow box) inactive. Increased external osmolarity leads to loss of turgor, inactivation of the phosphotransfer module, activation of the MAP kinase module, the output of which again activates the phosphotransfer module (via increased glycerol production and accumulation, leading to turgor recovery, but this part is excluded in this simplified scheme). (B) The update rules for states are derived from the reactions as described in the methods. (C) The update rules for reactions are derived from the contingencies, and also require that all components taking part in the reaction are present. (D) Screenshot from the rxncon Boolean simulation interface with the simplified HOG model. The left side shows the current state of each node, with false nodes appearing faded. Node states can be changed by selecting each node, or by selecting a state in the state plots to the right. The text based network definition (Additional_file_1) was pasted into the rxncon quick window and the simulator accessed via the ”Simulate Boolean” button. (E) State evolution of the simplified Hog model over two cycles displayed as heat map. Each row corresponds to a single elemental reaction or state, and the colours indicate active (Yellow; True) and inactive (Blue; False) nodes at each time step.