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

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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](http://www.plantphysiol.org/cgi/content/short/pp.110.167619?keytype=ref&ijkey=YTmfxrHG5QCsa8k)

(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)](http://link.springer.com/protocol/10.1007%2F978-1-62703-221-6_23),

[preprint](http://link.springer.com/protocol/10.1007%2F978-1-62703-221-6_23).

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)](http://www.springer.com/life+sciences/cell+biology/book/978-1-4939-1163-9).

Papers using VirtualLeaf

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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](http://arxiv.org/abs/1403.3926)

[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

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[Download the VirtualLeaf](https://drive.google.com/folderview?id=0B4SMVyYUsosrbVY3LTRXUHd5WWs&usp=sharing).