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Building Simulation Models of Developing Plant Organs Using VirtualLeaf

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

Abstract

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 

Notes

Acknowledgments

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.

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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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