It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
Fig 6
Comparing the ability of the fixed-rate and the two-step model to reproduce the dynamics of linear pathways that respond to different inputs.
Each pair of figures (A,B; C,D; …; K,L) demonstrates the performance of the two models for the different model inputs: impulse, piecewise constant, ramp, step, wave and noisy auto-activator, respectively (see Table 1). Figures A, C, E, G, I and K compares the optimised cost values (lower is better) for the fixed-rate model and the two-step model for each synthetic data set (5000 per input). Every data set is represented by a low-opacity dot; colour saturation thus indicates the density of similar values. Percentages indicate how often one model had a worse cost than the other. The orange dot shows the geometric median of the cost values for the different data sets. Figures B, D, F, H, J and L shows the model and data dynamics for the median data set of the corresponding input. The two-step model was chosen for the comparison since it has the same number of free parameters as the fixed-rate model.