Building Simulation Models of Developing Plant Organs Using VirtualLeaf

  • Roeland M. H. MerksEmail author
  • Michael A. Guravage
Part of the Methods in Molecular Biology book series (MIMB, volume 959)


Cell-based computational modeling and simulation are becoming invaluable tools in analyzing plant ­development. In a cell-based simulation model, the inputs are behaviors and dynamics of individual cells and the rules describe responses to signals from adjacent cells. The outputs are the growing tissues, shapes and cell-differentiation patterns that emerge from the local, chemical and biomechanical cell-cell interactions. Here, we present a step-by-step, practical tutorial for building cell-based simulations of plant development with VirtualLeaf, a freely available, open-source software framework for modeling plant development. We show how to build a model of a growing tissue, a reaction-diffusion system on a growing domain, and an auxin transport model. The aim of VirtualLeaf is to make computational modeling better accessible to experimental plant biologists with relatively little computational background.

Key words

Plant development Organ growth Cell division Cell growth Mathematical modeling Cell-based modeling Systems biology Computational modeling Reaction-diffusion Biomechanics Auxin 



This work was financed by the Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative/Netherlands Organisation for Scientific Research, and by Marie Curie European Reintegration Grant PERG03-GA-2008-230974 to RM.


  1. 1.
    Dupuy L, Mackenzie J, Rudge T, Haseloff J (2008) A system for modelling cell–cell interactions during plant morphogenesis. Ann Bot-London 101:1255–1265CrossRefGoogle Scholar
  2. 2.
    Grieneisen VA, Scheres B (2009) Back to the future: evolution of computational models in plant morphogenesis. Curr Opin Plant Biol 12:606–614PubMedCrossRefGoogle Scholar
  3. 3.
    Chickarmane V, Roeder AH, Tarr PT et al (2010) Computational morphodynamics: a modeling framework to understand plant growth. Annu Rev Plant Biol 61:65–87PubMedCrossRefGoogle Scholar
  4. 4.
    Santos F, Teale W, Fleck C et al (2010) Modelling polar auxin transport in developmental patterning. Plant Biol 12(Suppl 1):3–14PubMedCrossRefGoogle Scholar
  5. 5.
    Keurentjes JJ, Angenent GC, Dicke M et al (2011) Redefining plant systems biology: from cell to ecosystem. Trends Plant Sci 16:183–190PubMedCrossRefGoogle Scholar
  6. 6.
    Kitano H (2002) Systems biology: a brief overview. Science 295:1662–1664PubMedCrossRefGoogle Scholar
  7. 7.
    Merks RMH, Guravage M, Inzé D, Beemster GTS (2011) VirtualLeaf: An open-source framework for cell-based modeling of plant tissue growth and development. Plant Physiol 155:656–666PubMedCrossRefGoogle Scholar
  8. 8.
    Merks RMH, Glazier JA (2005) A cell-centered approach to developmental biology. Physica A 352:113–130CrossRefGoogle Scholar
  9. 9.
    Anderson ARA, Chaplain MAJ, Rejniak KA (eds.) (2007) Single-cell-based models in biology and medicine. Birkhaüser, BaselGoogle Scholar
  10. 10.
    Meinhardt H (1976) Morphogenesis of lines and nets. Differentiation 6:117–123PubMedCrossRefGoogle Scholar
  11. 11.
    Benítez M, Espinosa-Soto C, Padilla-Longoria P, Díaz J, Alvarez-Buylla ER (2007) Equivalent genetic regulatory networks in different contexts recover contrasting spatial cell patterns that resemble those in Arabidopsis root and leaf epidermis: a dynamic model. Int J Dev Biol 51:139–155PubMedCrossRefGoogle Scholar
  12. 12.
    Bouyer D, Geier F, Kragler F, Schnittger A, Pesch M, Wester K, Balkunde R, Timmer J, Fleck C, Hülskamp M (2008) Two-dimensional patterning by a trapping/depletion mechanism: the role of TTG1 and GL3 in Arabidopsis trichome formation. PLoS Biol 6:1166–1177CrossRefGoogle Scholar
  13. 13.
    Merks RMH, Van de Peer Y, Inzé D, Beemster GTS (2007) Canalization without flux sensors: a traveling-wave hypothesis. Trends Plant Sci 12:384–390PubMedCrossRefGoogle Scholar
  14. 14.
    Jönsson H, Heisler MG, Shapiro BE, Meyerowitz EM, Mjolsness E (2006) An auxin-driven polarized transport model for phyllotaxis. P Natl Acad Sci USA 103: 1633–1638CrossRefGoogle Scholar
  15. 15.
    Smith RS, Guyomarc’h S, Mandel T, Reinhardt D, Kuhlemeier C, Prusinkiewicz P (2006) A plausible model of phyllotaxis. P Natl Acad Sci USA 103:1301–1306CrossRefGoogle Scholar
  16. 16.
    Ellner SP, Guckenheimer J (2006) Dynamic models in biology. Princeton University Press, PrincetonGoogle Scholar
  17. 17.
    Fall CP, Wagner JM, Marland ES, Tyson JJ (eds) (2002) Computational cell biology. Series interdisciplinary applied mathematics, vol 20. Springer, New YorkGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Centrum Wiskunde & Informatica (CWI)XG AmsterdamThe Netherlands
  2. 2.Netherlands Consortium for Systems Biology/Netherlands Institute for Systems Biology (NCSB-NISB)XG AmsterdamThe Netherlands

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