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Software developed by the Biomodeling & Biosystems Analysis group

For our computational research on collective cell behavior during biological development, we routinely develop simulation codes that we are releasing as open source. If you want to model plant tissues, please use our vertex-based cell-based simulation software VirtualLeaf. If plan to model animal tissues, use Tissue Simulation Toolkit, a two-dimensional implementation of the Cellular Potts Model. 

Apart from developing our own codes for the Cellular Potts Model, we increasingly make use of the excellent open source package CompuCell3D.  The Tissue Simulation Toolkit is a relatively small and straightforward C++ library, making it well suited for developing new ideas and algorithms. CompuCell3D is well suited for constructing new biological models based on existing technology and minor extensions in the form of ``plugins''. Check back soon for releases of CompuCell3D plugins that we have developed in our research.

 

 

VirtualLeaf

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.

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.

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).

 

Publications using VirtualLeaf

  • Mellor, N., Adibi, M., El-Showk, S., De Rybel, B., King, J., Mähönen, A.P., Weijers, D., Bishopp, A. (2016) Theoretical approaches to understanding root vascular patterning: a consensus between recent models. J Exp Bot, advanced acces. doi:10.1093/jxb/erw410
  • Dzhurakhalov, A. (2015). Modelling plant cell expansion  in VirtualLeaf. PhD Thesis. University of Antwerp. http://gradworks.umi.com/36/64/3664579.html
  • 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
  • Draelants, D., Avitabile, D. & Vanroose, W. (2015) Localised auxin peaks in concentration-based transport models for plants. J. Roy. Soc. Interface 12(106):20141407. doi:10.1186/1752-0509-4-98
  • 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


Recent downloads can be obtained from
https://drive.google.com/folderview?id=0B4SMVyYUsosrbVY3LTRXUHd5WWs&usp=sharing


Also see our page on GoogleCode.


Tissue Simulation Toolkit

Tissue Simulation Toolkit (TST) is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms. Download the Tissue Simulation Toolkit software here.

 

Papers on Tissue Simulation Toolkit


We first mentioned the tissue simulation toolkit in: R M H Merks, & J A Glazier. (2005). A cell-centered approach to developmental biology. Physica A, 352(1), 113–130. doi:10.1016/j.physa.2004.12.028. Please cite that paper and the SourceForge website if you use the TST in your work.

A detailed step by step tutorial will be available in
Josephine T. Daub and Roeland M. H. Merks. Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit. In: Vascular Morphogenesis. Domenico Ribatti (Ed.) Methods in Molecular Biology, in press.

Papers using Tissue Simulation Toolkit

 

  • Daub, J. T., & Merks, R. M. H. (2013). A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis. Bull Math Biol, 75(8), 1377–1399. doi:10.1007/s11538-013-9826-5
  • Szabó, A., Varga, K., Garay, T., Hegedűs, B., & Czirok, A. (2012). Invasion from a cell aggregate--the roles of active cell motion and mechanical equilibrium. Physical Biology, 9(1), 016010–016010. doi:10.1088/1478-3975/9/1/016010
  • Szabó, A., Unnep, R., Méhes, E., Twal, W. O., W S Argraves, Cao, Y., & A Czirók. (2010). Collective cell motion in endothelial monolayers. Physical Biology, 7(4), 046007. doi:10.1088/1478-3975/7/4/046007
  • Scianna, M., Roeland M H Merks, Preziosi, L., & Medico, E. (2009). Individual cell-based models of cell scatter of ARO and MLP-29 cells in response to hepatocyte growth factor. Journal of Theoretical Biology, 260(1), 151–160. doi:10.1016/j.jtbi.2009.05.017
  • Szabó, A., & Czirok, A. (2010). The Role of Cell-Cell Adhesion in the Formation of Multicellular Sprouts. Mathematical Modelling of Natural Phenomena, 5(1), 106–122. doi:10.1051/mmnp/20105105
  • Merks, R. M. H., Perryn, E. D., Shirinifard, A., & Glazier, J. A. (2008). Contact-inhibited chemotaxis in de novo and sprouting blood-vessel growth. PLoS Comp Biol, 4(9), e1000163. doi:10.1371/journal.pcbi.1000163
  • Szabó, A., Mehes, E., Kosa, E., & Czirok, A. (2008). Multicellular sprouting in vitro. Biophysical Journal, 95(6), 2702–2710. doi:10.1529/biophysj.108.129668
  • Savill, N. J., & Merks, R. M. H. (2007). The Cellular Potts Model in Biomedicine. In A. R. A. Anderson, M. A. J. Chaplain, & K. A. Rejniak, Single-Cell-Based Models in Biology and Medicine (pp. 137–150). Birkhaüser Verlag.
  • Merks, R. M. H., Brodsky, S. V., Goligorksy, M. S., Newman, S. A., & Glazier, J. A. (2006). Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. Developmental Biology, 289(1), 44–54. doi:10.1016/j.ydbio.2005.10.003
  • Merks, R. M. H., & Glazier, J. A. (2006). Dynamic mechanisms of blood vessel growth. Nonlinearity, 19(1), C1–C10. doi:10.1088/0951-7715/19/1/000
  • Merks, R. M. H., Newman, S. A., & Glazier, J. A. (2004). Cell-oriented modeling of in vitro capillary development. Lect. Notes Comput. Sci., 3305, 425–434.