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](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
------------------------
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).