Dynamic profile of the EGF/TNFα model. The model was simulated with consistent results in the Cell Collective (on the left of panels A & B), GINsim (on the right of panels A & B), and CellNOpt (data not shown, but simulations were consistent with those presented here). Synchronous simulations were performed under four input conditions: (i) EGF = TNFα = 0; (ii) EGF = TNFα = 1; (iii) EGF = 0 & TNFα = 1; (iv) EGF = 1 & TNFα = 0. Results for conditions in (i) and (ii) are presented in this figure (the remaining two can be found in Additional file 1). Charts on the top left of each panel correspond to the overall dynamic profile across all nodes in the model. Black cells correspond to active (1) states, whereas inactive (0) states are white. The bottom graphs at the bottom left illustrate the time course of selected nodes. The GINsim columns show State Transition Graph and the Hierarchical Transition Graph (HTG) generated with the tool. Note that due to the synchronous updating, the irreversible components of the (HTG) correspond to linear chains of states. A) EGF = TNFα = 0. The network reaches a steady state (shown with both GINsim and the Cell Collective) after 3 transient states. The order of the individual species states in the steady state generated by GINsim is sorted in the same (alphabetical) order, as presented on the Cell Collective side. B) EGF = TNFα = 1. After 12 transient states, the network reaches a cyclical attractor encompassing six states. Note that in order to simulate the example model in the Cell Collective as a traditional Boolean network (i.e., with binary input/output), the external species were set to 100 or 0, and the sliding window was set to 1 (see Methods).