Cell-based computational modeling and simulation are becoming invaluable tools in analyzing plant development. In a cell-based simulation model, the inputs are behaviors and dynamics of individual cells and the rules describing responses to signals from adjacent cells. The outputs are the growing tissues, shapes and cell-differentiation patterns that emerge from the local, chemical and biomechanical cell-cell interactions. Here, we present a step-by-step, practical tutorial for building cell-based simulations of plant development with VirtualLeaf, a freely available, open-source software framework for modeling plant development. We show how to build a model of a growing tissue, a reaction-diffusion system on a growing domain, and an auxin transport model. The aim of VirtualLeaf is to make computational modeling better accessible to experimental plant biologists with relatively little computational background.
Additional Metadata
THEME Life Sciences (theme 5), Energy (theme 4)
Publisher Springer
Editor I. de Smet
Series Methods in Molecular Biology
Project Integrating modeling into plant systems biology: Applications to auxin-driven plant morphogenesis
Note in press
Citation
Merks, R.M.H, & Guravage, M.A. (2012). Building simulation models of developing plant organs using VirtualLeaf. In I de Smet (Ed.), Plant Organogenesis . Springer.