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VirtualLeaf: an Open Source framework for cell-based modeling of plant tissue growth and development

Roeland M. H. Merks, Michael Guravage, Dirk Inzé, Gerrit T.S. Beemster. VirtualLeaf: an Open Source framework for cell-based modeling of plant tissue growth and development. Plant Physiology, doi:10.1104/pp.110.167619.

Plant organs, including leaves and roots, develop by means of a multi-level crosstalk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multi-level regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the role of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically-intuitive in silico objects (cells, regulation networks) required for setting up a simulation, and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer-modeling framework VirtualLeaf for plant tissue morphogenesis. The current version defines a set of biologically-intuitive C++ objects, including cells, cell walls, and diffusing and reacting chemicals, that provide useful abstractions for building biological simulations of developmental processes. We present a step-by-step introduction to building models with the VirtualLeaf, providing basic example models of leaf venation and meristem development. VirtualLeaf-based models provide a means for plant researchers to analyze the function of developmental genes in the context of the biophysics of growth and patterning. The VirtualLeaf is an ongoing Open Source software project that runs on Windows, Mac and Linux.  doi:10.1104/pp.110.167619