Figure 2.

Examples of hypothesis-driven bottom-up and middle-out approaches. Models were constructed for processes at different spatial and temporal scales. A, At the subcellular level, GRNs can be modeled to include the input of signals such as auxin and output in the form of cell-scale events, such as mitosis. B, Stem cell division and the bistable switch that regulates it are modeled using longitudinal gradients of auxin and radial gradients of the transcription factor SHR (Cruz-Ramírez et al., 2012). C, Root system scale models such as RootTyp (Pagès et al., 2004) can be linked to hydraulic models to explicitly simulate water flow in the soil-plant domain (Javaux et al., 2008).