Mathematical modeling has become increasingly adopted in analyzing the dynamics of biological systems at diverse length- and time-scales1,2,3,4,5,6. In each case, a model is typically formulated to account for the biological processes underlying the system dynamics of interest. When analyzing a gene circuit, the corresponding model often entails description of the gene expression; for a metabolic pathway, the corresponding model may describe the constituent enzymatic reactions; for an ecosystem, the corresponding model would describe growth, death, and movement of individual populations, which could in turn be influenced by other populations. We call these models mechanism-based models. Mechanism-based models are useful for testing our understanding of the systems of interest7,8,9,10,11,12,13,14.