Examples of simulations in the Cell Collective. In panels A-C, the model was simulated 100 times, 800 time steps each. For each of the 100 simulations, an activity level between 0 and 100 (i.e., probability of being active at time t) was randomly selected for EGF (panels A and B) and TNFα (panel C). A) Dose–response curve illustrating the activation of Akt under changing levels of EGF. B) Inhibition of PI3K results in the loss of EGF-induced activation of Akt. C) Dose–response curve illustrating inactivation of IkB in response to increasing levels of TNFα. D-F) Real-time simulation under varying conditions: D) Setting EGF to 50% (using the sliders illustrated above the plot) results in an intermediate activation of Akt, and transient activation of Ras and Erk. E) Simulated Ras gain-of-function (introduced around time step 50), results in the activation of Ras, which subsequently stimulates Erk. Akt remains active at around 50%. F) The removal of EGF (turning it to 0%) results in the decrease of Akt activity, while Erk continues to rise due to Ras mutation. Any and all species in the model can be displayed during the real-time simulations; the three species Akt, Erk, and Ras were selected for illustration purposes only. Note that the activation levels do not correspond to concentrations or any molecular measurements; they rather provide a semi-quantitative activity measure to analyse the effects of changes in the model (e.g., perturbations) on the rest of the network.