Advanced search
1 file | 1.46 MB Add to list

VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development

Roeland Merks (UGent) , Michael Guravage, Dirk Inzé (UGent) and Gerrit Beemster (UGent)
(2011) PLANT PHYSIOLOGY. 155(2). p.656-666
Author
Organization
Project
Biotechnology for a sustainable economy (Bio-Economy)
Abstract
Plant organs, including leaves and roots, develop by means of a multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically intuitive in silico objects ("cells", "regulation networks") required for setting up a simulation and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer modeling framework VirtualLeaf 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. We present a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development. 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. VirtualLeaf is an ongoing open-source software project (http://virtualleaf.googlecode.com) that runs on Windows, Mac, and Linux.
Keywords
AUXIN TRANSPORT, ARABIDOPSIS ROOT, MATHEMATICAL MODELS, PATTERN, MORPHOGENESIS, PHYLLOTAXIS, ELONGATION, SUFFICIENT, SIMULATION, EXPRESSION

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 1.46 MB

Citation

Please use this url to cite or link to this publication:

MLA
Merks, Roeland, Michael Guravage, Dirk Inzé, et al. “VirtualLeaf: An Open-source Framework for Cell-based Modeling of Plant Tissue Growth and Development.” PLANT PHYSIOLOGY 155.2 (2011): 656–666. Print.
APA
Merks, R., Guravage, M., Inzé, D., & Beemster, G. (2011). VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development. PLANT PHYSIOLOGY, 155(2), 656–666.
Chicago author-date
Merks, Roeland, Michael Guravage, Dirk Inzé, and Gerrit Beemster. 2011. “VirtualLeaf: An Open-source Framework for Cell-based Modeling of Plant Tissue Growth and Development.” Plant Physiology 155 (2): 656–666.
Chicago author-date (all authors)
Merks, Roeland, Michael Guravage, Dirk Inzé, and Gerrit Beemster. 2011. “VirtualLeaf: An Open-source Framework for Cell-based Modeling of Plant Tissue Growth and Development.” Plant Physiology 155 (2): 656–666.
Vancouver
1.
Merks R, Guravage M, Inzé D, Beemster G. VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development. PLANT PHYSIOLOGY. 2011;155(2):656–66.
IEEE
[1]
R. Merks, M. Guravage, D. Inzé, and G. Beemster, “VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development,” PLANT PHYSIOLOGY, vol. 155, no. 2, pp. 656–666, 2011.
@article{1209192,
  abstract     = {Plant organs, including leaves and roots, develop by means of a multilevel cross talk between gene regulation, patterned cell division and cell expansion, and tissue mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological development, because these methodologies implicitly assume a direct relation between genes and traits at the level of the whole plant or organ. Instead, understanding gene function requires insight into the roles of gene products in regulatory networks, the conditions of gene expression, etc. This interplay is impossible to understand intuitively. Mathematical and computer modeling allows researchers to design new hypotheses and produce experimentally testable insights. However, the required mathematics and programming experience makes modeling poorly accessible to experimental biologists. Problem-solving environments provide biologically intuitive in silico objects ("cells", "regulation networks") required for setting up a simulation and present those to the user in terms of familiar, biological terminology. Here, we introduce the cell-based computer modeling framework VirtualLeaf 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. We present a step-by-step introduction to building models with VirtualLeaf, providing basic example models of leaf venation and meristem development. 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. VirtualLeaf is an ongoing open-source software project (http://virtualleaf.googlecode.com) that runs on Windows, Mac, and Linux.},
  author       = {Merks, Roeland and Guravage, Michael and Inzé, Dirk and Beemster, Gerrit},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  keywords     = {AUXIN TRANSPORT,ARABIDOPSIS ROOT,MATHEMATICAL MODELS,PATTERN,MORPHOGENESIS,PHYLLOTAXIS,ELONGATION,SUFFICIENT,SIMULATION,EXPRESSION},
  language     = {eng},
  number       = {2},
  pages        = {656--666},
  title        = {VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development},
  url          = {http://dx.doi.org/10.1104/pp.110.167619},
  volume       = {155},
  year         = {2011},
}

Altmetric
View in Altmetric
Web of Science
Times cited: