In the recent years, much research work in molecular and developmental biology has been devoted to unravel the mechanisms that govern living systems development. This includes the identification of key molecular networks that control shape formation and their response to hormonal regulation. However, a key challenge now is to understand how these signals that arise at cellular scale are physically translated into shape changes and growth at organ scale and how this interpretation process feeds back into molecular regulation systems. Technology is remarkably rapidly accompanying this investigation, leading recently, for example, to very efficient ways of reconstructing the geometry of every cell in 3D in growing tissues or of measuring estimates of wall mechanical properties with unprecedented accuracy. To integrate and interpret these data, we now need to develop 3D quantitative models that are able to relate cell mechanics, 3D geometry and gene regulation. In this talk, I will present a mathematical framework of the development of a 3D virtual tissue with cell resolution, where a growth equation is used to express gene function in terms of wall elasticity, wall synthesis, turgor-pressure and the expansion threshold above which wall synthesis is triggered. Novel computational approaches based on finite element method make it possible to perform simulations in near real-time. Using this framework, we provide a qualitative analysis of flower development, showing, for example, how regulation of regional identities can lead to realistic shape development.