We describe an ongoing project which aims at a better understanding of the development and functioning of apple trees by modelling them at several spatial and temporal scales. Dependence of growth and carbon allocation upon genotype, environmental variables (particularly, water supply), fruit load and experimental manipulation of carbon transport is investigated and simulated. For the required functional-structural models, new tools are developed, especially for handling multiple-scale representations of the same organism in a user-friendly way, for cross-platform modelling and for facilitating the application of rigorous methods of parameter estimation and sensitivity analysis.