Building Simulation Models of Developing Plant Organs Using VirtualLeaf
- 2.8k Downloads
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 wordsPlant 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.
- 9.Anderson ARA, Chaplain MAJ, Rejniak KA (eds.) (2007) Single-cell-based models in biology and medicine. Birkhaüser, BaselGoogle Scholar
- 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
- 16.Ellner SP, Guckenheimer J (2006) Dynamic models in biology. Princeton University Press, PrincetonGoogle Scholar
- 17.Fall CP, Wagner JM, Marland ES, Tyson JJ (eds) (2002) Computational cell biology. Series interdisciplinary applied mathematics, vol 20. Springer, New YorkGoogle Scholar