Overview

VirtualLeaf is a cell-based computer-modeling framework 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. 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? runs on Windows, Mac and Linux.

Papers on VirtualLeaf

If you use VirtualLeaf in your work, please cite our paper Merks, R. M. H., Guravage, M., Inzé, D., & Beemster, G. T. S. (2011). VirtualLeaf: An Open-Source Framework for Cell-Based Modeling of Plant Tissue Growth and Development. Plant Phys., 155(2), 656–666 (Open Access).

A step-by-step introduction to building models with the VirtualLeaf?, providing basic example models of leaf venation and meristem development, is available in Merks, R. M. H., & Guravage, M. A. (2012). Building Simulation Models of Developing Plant Organs Using VirtualLeaf. In Methods in Molecular Biology (Vol. 959, pp. 333–352), preprint. A list of problems, issues, and solutions re: this book chapter is maintained on googlecode.

If need assistance in setting up parameter studies for your model, please see our chapter Palm, M.M., & Merks, R.M.H. (2014). Large-Scale Parameter Studies of Cell-Based Models of Tissue Morphogenesis Using CompuCell3D or VirtualLeaf. In Methods in Molecular Biology (Vol. 1189).

Papers using VirtualLeaf

Dirk De Vos, Kris Vissenberg, Jan Broeckhove, Gerrit T. S. Beemster (2014). Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root? PLoS Computational Biology, 10(10), e1003910. doi:10.1371/journal.pcbi.1003910

De Rybel, B., Adibi, M., Breda, A. S., Wendrich, J. R., Smit, M. E., Novák, O., et al. (2014). Integration of growth and patterning during vascular tissue formation in Arabidopsis. Science (New York, NY), 345(6197), 1255215–1255215. doi:10.1126/science.1255215

D. Draelants, D. Avitabile, & W. Vanroose, Localised auxin peaks in concentration-based transport models for plants [arXiv:1403.3926].

Van Mourik, S., Kaufmann, K., Van Dijk, A. D. J., Angenent, G. C., Merks, R. M. H., & Molenaar, J. (2012). Simulation of Organ Patterning on the Floral Meristem Using a Polar Auxin Transport Model. PLoS ONE, 7(1), e28762. doi:10.1371/journal.pone.0028762.s018

Wabnik, K., Kleine-Vehn, J., Balla, J., Sauer, M., Naramoto, S., Reinöhl, V., et al. (2010). Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling. Molecular Systems Biology, 6, 447. doi:10.1038/msb.2010.103

R M H Merks, Van de Peer, Y., Inzé, D., & Beemster, G. T. S. (2007). Canalization without flux sensors: a traveling-wave hypothesis. Trends in Plant Science, 12(9), 384–390. doi:10.1016/j.tplants.2007.08.004

Downloads

Download the VirtualLeaf.