Fig. 3

Comparison of simulation-based predictions made by using SimBoolNet, GINsim and the proposed simulator. Two different inputs are used: (1) EGFR and TNFR are perturbed at the beginning of the simulation with input levels 0.5 and 0.8, respectively, and (2) EGFR is inhibited at the 10th iteration with input level -1 and TNFR is activated at the 20th iteration with input level 0.8. The edge weights of activation and blockage are set to 0.7 and 0.8, respectively, for both inputs. The simulation is executed for 100 iterations. a–c The plots of simulation results using the proposed model for EGFR, TNFR and ERK, under two different inputs. d–f The plots of SimBoolNet results under input 1 and 2, respectively. Please note that the two curves are totally overlap for TNFR in (e). g–i GINsim simulation results for EGFR, TNFR and ERK. Each run of GINsim simulation executes 8 iterations before reaching the stable state