Modeling Plant Tissue Development Using VirtualLeaf

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. In this updated and extended version of our previous chapter on VirtualLeaf (Merks and Guravage, Methods in Molecular Biology 959, 333-352), we present a step-by-step, practical tutorial for building cell-based simulations of plant development and for analyzing the influence of parameters on simulation outcomes by systematically changing the values of the parameters and analyzing each outcome. We show how to build a model of a growing tissue, a reaction-diffusion system on a growing domain, and an auxin transport model. Moreover, in addition to the previous publication, we demonstrate how to run a Turing system on a regular, rectangular lattice, and how to run parameter sweeps. The aim of VirtualLeaf is to make computational modeling more accessible to experimental plant biologists with relatively little computational background.