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Modeling Plant Tissue Development Using VirtualLeaf

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Plant Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2395))

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 describing 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. In this updated and extended version of our previous chapter on VirtualLeaf (Merks and Guravage, Methods in Molecular Biology 959, 333–352), we present a step-by-step, practical tutorial for building cell-based simulations of plant development and for analyzing the influence of parameters on simulation outcomes by systematically changing the values of the parameters and analyzing each outcome. We show how to build a model of a growing tissue, a reaction–diffusion system on a growing domain, and an auxin transport model. Moreover, in addition to the previous publication, we demonstrate how to run a Turing system on a regular, rectangular lattice, and how to run parameter sweeps. The aim of VirtualLeaf is to make computational modeling more accessible to experimental plant biologists with relatively little computational background.

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Acknowledgments

We thank Robbert Geerts from the VU Amsterdam and Rosalie Althuis of Leiden University for their useful feedback on difficulties encountered throughout the usage of VirtualLeaf for their master’s thesis and bachelor’s thesis projects. This work was funded by the Leiden/Huygens Fellowship (C.-C. A.), the Leiden University Fund under grant number W213078-1 (G.Y.P), and the Netherlands Organization for Scientific Research (NWO-ENW) within the Innovational Research Incentives Scheme (R. M. H. M.; Vici 2017, No. 865.17.004).

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Authors and Affiliations

  1. Mathematical Institute, Leiden University, Leiden, The Netherlands

    Claudiu-Cristi Antonovici, Guacimo Y. Peerdeman & Roeland M. H. Merks

  2. Institute of Biology, Leiden University, Leiden, The Netherlands

    Claudiu-Cristi Antonovici, Guacimo Y. Peerdeman & Roeland M. H. Merks

  3. Faculty of Science and Technology, University of Applied Sciences Leiden, Leiden, The Netherlands

    Guacimo Y. Peerdeman

  4. Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, VUmc, Amsterdam, The Netherlands

    Harold B. Wolff

Authors
  1. Claudiu-Cristi Antonovici
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  2. Guacimo Y. Peerdeman
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  3. Harold B. Wolff
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  4. Roeland M. H. Merks
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Corresponding author

Correspondence to Roeland M. H. Merks .

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Editors and Affiliations

  1. DIADE, Univ Montpellier, IRD,, CIRAD, Montpellier, France

    Mikaël Lucas

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Antonovici, CC., Peerdeman, G.Y., Wolff, H.B., Merks, R.M.H. (2022). Modeling Plant Tissue Development Using VirtualLeaf. In: Lucas, M. (eds) Plant Systems Biology. Methods in Molecular Biology, vol 2395. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1816-5_9

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  • DOI: https://doi.org/10.1007/978-1-0716-1816-5_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1814-1

  • Online ISBN: 978-1-0716-1816-5

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