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Building simulation models of developing plant organs using VirtualLeaf

Roeland M.H. Merks and Michael Guravage. Building simulation models of developing plant organs using VirtualLeaf. In: De Smet, I. (Ed.) Methods in Molecular Biology, vol. 959: Plant Organogenesis, pp. 333-352, Springer-Verlag Berlin Heidelberg, 2013

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. 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. In: Ive de Smet (Ed.) Methods in Molecular Biology, vol. 959 Plant Organogenesis, Springer-Verlag Berlin Heidelberg, pp. 333-352. Also see preprint.