Team Virtual Plants

Overall Objectives
Scientific Foundations
New Results
Other Grants and Activities


Major publications by the team in recent years

P. Barbier de Reuille, I. Bohn-Courseau, K. Ljung, H. Morin, N. Carraro, C. Godin, J. Traas.
Computer simulations reveal novel properties of the cell-cell signaling network at the shoot apex in Arabidopsis, in: PNAS, 2006, vol. 103, p. 1627-1632
J.-B. Durand, P. Gonçalvès, Y. Guédon.
Computational methods for hidden Markov tree models - An application to wavelet trees, in: IEEE Transactions on Signal Processing, 2004, vol. 52, no 9, p. 2551-2560.
J.-B. Durand, Y. Guédon, Y. Caraglio, E. Costes.
Analysis of the plant architecture via tree-structured statistical models: the hidden Markov tree models., in: New Phytol, Jun 2005, vol. 166, no 3, p. 813–825
P. Ferraro, C. Godin.
An edit distance between quotiented trees, in: Algorithmica, 2003, vol. 48, p. 385-406.
P. Ferraro, C. Godin, P. Prusinkiewicz.
Toward a quantification of self-similarity in plants, in: Fractals, 2005, vol. 13, no 2, p. 91-109
C. Godin, Y. Caraglio.
A multiscale model of plant topological structures, in: Journal of Theoretical Biology, 1998, vol. 191, p. 1-46
C. Godin, E. Costes, H. Sinoquet.
Plant architecture modelling - virtual plants and complex systems, in: Plant Architecture and its Manipulation, C. Turnbull (editor), Annual plant reviews, Blackwell, 2005, vol. 17, p. 238-287
Y. Guédon, Y. Caraglio, P. Heuret, E. Lebarbier, C. Meredieu.
Analyzing growth components in trees, in: Journal of Theoretical Biology, 2007, vol. 248, no 3, p. 418–447
Y. Guédon, D. Barthelemy, Y. Caraglio, E. Costes.
Pattern analysis in branching and axillary flowering sequences, in: Journal of Theoretical Biology, 2001, vol. 212, p. 481-520.
Y. Guédon.
Estimating hidden semi Markov chains from discrete sequences, in: Journal of Computational and Graphical Statistics, 2003, vol. 12, no 3, p. 604-639.

Publications of the year

Articles in International Peer-Reviewed Journal

F. Chaubert - Pereira, Y. Caraglio, C. Lavergne, Y. Guédon.
Identifying ontogenetic, environmental and individual components of forest tree growth., in: Annals of Botany, 2009, vol. 104, no 5, p. 883–896
F. Chaubert - Pereira, Y. Guédon, C. Lavergne, C. Trottier.
Markov and semi-Markov switching linear mixed models used to identify forest tree growth components., in: Biometrics, 2009
E. Farcot, J.-L. Gouzé.
Periodic Solutions of Piecewise Affine Gene Network Models with Non Uniform Decay Rates: The Case of a Negative Feedback Loop, in: Acta Biotheoretica, 2009, vol. 57, no 4, p. 429–455
S. Mondet, W. Cheng, G. Morin, R. Grigoras, F. Boudon, W. Tsang Ooi.
Compact and Progressive Plant Models for Streaming in Networked Virtual Environments, in: ACM Transactions on Multimedia Computing, Communications, and Applications (TOMCCAP), aug 2009, vol. 5, no 3, p. 1–22
C. Pradal, F. Boudon, C. Nouguier, J. Chopard, C. Godin.
PlantGL : a Python-based geometric library for 3D plant modelling at different scales, in: Graphical Models, jan 2009, vol. 71, no 1, p. 1–21

International Peer-Reviewed Conference/Proceedings

A. Doran, S. Mondet, R. Grigoras, G. Morin, W. Tsang Ooi, F. Boudon.
A Demonstration of MobiTree: Progressive 3D Tree Models Streaming on Mobile Clients, in: ACM Multimedia 2009, Beijing, ACM, oct 2009
J. Wither, F. Boudon, M.-P. Cani, C. Godin.
Structure from silhouettes: a new paradigm for fast sketch-based design of trees, in: Computer Graphic Forum. Special issue: Eurographics 2009, 2009, vol. 28 (2), p. 541–550
D.-M. Yan, J. Wintz, B. Mourrain, W. Wang, F. Boudon, C. Godin.
Efficient and robust reconstruction of botanical branching structure from laser scanned points, in: 11th IEEE International conference on Computer-Aided Design and Computer Graphics (CAD/Graphics 2009), 2009

Workshops without Proceedings

T. Cokelaer, C. Pradal, C. Fournier.
Plant modelling with Python components in OpenAlea, in: EuroSciPy 2009, 2009

Internal Reports

E. Farcot, J.-L. Gouzé.
Limit cycles in piecewise-affine gene network models with multiple interaction loops, INRIA, Mar 2009, no RR-6875, INRIA Research Report.
E. Farcot, J.-L. Gouzé.
Qualitative control of periodic solutions in piecewise affine systems; application to genetic networks, INRIA, Dec 2009, no RR-7130, INRIA Research Report.

References in notes

A. Arber.
Natural philosophy of plant form, University Press, Cambridge, 1950.
D. Barthelemy, Y. Caraglio, E. Costes.
Architecture, gradients morphogénétiques et âge physiologique chez les végétaux, in: Modélisation et Simulation de l'Architecture des Végétaux, J. Bouchon, P. de Reffye, D. Barthelemy (editors), 1997, p. 89-136.
E. Costes, C. Smith, M. Renton, Y. Guédon, P. Prusinkiewicz, C. Godin.
MAppleT: simulation of apple tree development using mixed stochastic and biomechanical models, in: Functional Plant Biology, 2008, vol. 35, no 9 & 10, p. 936–950
P. Ferraro, C. Godin.
A distance measure between plant architectures, in: Annals of Forest Science, 2000, vol. 57, no 5/6, p. 445-461
D. Fumey, P. Lauri, Y. Guédon, C. Godin, E. Costes.
Effects of pruning on the apple tree: from tree architecture to modeling, in: International Symposium on Integrating Canopy, Rootstock and Environmental Physiology in Orchard Systems, 2008
L. E. Gatsuk, O. V. Smirnova, L. I. Vorontzova, L. B. Zaugolnova, L.A. Zhukova.
Age states of plants of various growth forms: a review, in: Journal of Ecology, 1980, vol. 68, p. 675-696.
C. Godin, E. Costes, H. Sinoquet.
A method for describing plant architecture which integrates topology and geometry, in: Annals of Botany, 1999, vol. 84, p. 343-357.
Y. Guédon, Y. Caraglio, P. Heuret, E. Lebarbier, C. Meredieu.
Analyzing growth components in trees, in: Journal of Theoretical Biology, 2007, vol. 248, no 3, p. 418–447
F. Hallé, R. A. A. Oldeman, P. B. Tomlinson.
Tropical trees and forests. An architectural analysis, Springer-Verlag, New-York, 1978.
J. L. Harper, B. R. Rosen, J. White.
The growth and form of modular organisms, The Royal Society, London, UK, 1986.
H. Jönsson, M. Heisler, G. V. Reddy, V. Agrawal, V. Gor, B. E. Shapiro, E. Mjolsness, E. M. Meyerowitz.
Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem, in: Bioinformatics, 2005, vol. 21, no 1, p. 232–240
M. Lucas, Y. Guédon, C. Jay-Allemand, C. Godin, L. Laplaze.
An auxin transport-based model of root branching in Arabidopsis thaliana, in: PLoS ONE, 2008, vol. 3, no 11
M. Lucas.
Etude et modélisation des déterminismes de mise en place et de développement des racines latérales chez Arabidopsis Thaliana , Université Montpellier II, 2008, Ph. D. Thesis.
S. Mondet, W. Cheng, G. Morin, R. Grigoras, F. Boudon, W. Tsang Ooi.
Streaming of Plants in Distributed Virtual Environments, in: ACM Multimedia 2008 - Systems and Networking Track, 2008
R. Nozeran.
Integration of organismal development, in: Positional controls in plant development, P. Barlow, D. Carr (editors), 1984, p. 375-401.
D. Reinhardt, E.-R. Pesce, P. Stieger, T. Mandel, K. Baltensperger, M. Bennett, J. Traas, J. Friml, C. Kuhlemeier.
Regulation of phyllotaxis by polar auxin transport, in: Nature, November 2003, vol. 426, no 6964, p. 255–260
M. Renton, Y. Guédon, C. Godin, E. Costes.
Similarities and gradients in growth-unit branching patterns during ontogeny in Fuji apple trees: A stochastic approach., in: Journal of Experimental Botany, 2006, vol. 57, no 12, p. 3131–3143
A. Runions, B. Lane, P. Prusinkiewicz.
Modeling Trees with a Space Colonization Algorithm, in: Eurographics Workshop on Natural Phenomena, 2007, p. 63-70
H. Sinoquet, P. Rivet, C. Godin.
Assessment of the three-dimensional architecture of walnut trees using digitizing, in: Silva Fennica, 1997, vol. 3, p. 265–273.