Section: Other Grants and Activities
Agropolis computational plant seminar
Participants : Yann Guédon, Christine Granier [ INRA, LEPSE ] , Laurent Laplaze [ IRD, DIAPC ] .
Funding: Agropolis fundation (Contractor for Virtual Plants: CIRAD. From 2008 to 2011)
In the context of the creation of a world-level pole on plant science in the region Languedoc-Roussillon, we organize a monthly seminar and a yearly workshop at Agropolis (see http://www.plantnum.agropolis.fr ). The 2009 one-day workshop was devoted to models at the cellular and tissular scales and the invited speakers were J. Haseloff (U. Cambridge), N. Bertin (PSH, INRA), E. Mjolsness (UC. Irvine), N. Monk (U. Nottingham), E. Bayer (Institute of Plant Sciences, Berne) and T. Vernoux (RDP, CNRS). The seminar is organized by Yann Guédon, Christine Granier (INRA, LESPE) and Laurent Laplaze (IRD, DIAPC) with the support of Agropolis International and Agropolis Foundation.
Advanced Markovian techniques in population dynamics
Participant : Yann Guédon.
Funding: University Montpellier 2 (Contractor for Virtual Plants: CIRAD. From 2008 to 2009)
The objective of this joined project with Centre d'Écologie Fonctionnelle et Evolutive, (BIOSTIC project, University Montpellier 2) is to adapt hidden semi-Markov models to population dynamic problems.
Participants : Christophe Pradal, Christophe Godin, Christian Fournier [ INRA, LEPSE ] .
Funding: Agropolis fundation (Contractors for Virtual Plants: CIRAD and INRIA from 2009 to 2011)
The aim of this project is to foster the development and the national and international diffusion of the platform OpenAlea. This opensource plateform provides an easy-to-use environment for plant modellers through a visual programming interface to efficiently use and combine models or computational methods from different scientific fields in order to represent, analyse and simulate complex plant systems at different scales, from meristems to plant canopy. OpenAlea makes it possible to assemble highly reusable, heterogeneous components. The central point of its architecture is to allow to integrate existing components or modules developed by different teams without rewriting them. These components are developed in multi-languages like C, C++, Fortran or Java as well as Python. Work comprises development of standard data structures, deployment tools, documentation, training, software engineering, user interface, ...
Participants : Eric Moscardi, ,Christophe Pradal, Christophe Godin, Grégoire Malandain [ INRIA, Asclepios ] .
Funding: INRIA (Contractors for Virtual Plants: INRIA from 2009 to 2011)
The goal of this project is to integrate in a single software platform all the software tools and algorithms that have been developed in various projects about meristem modelling in our teams. More precisely, we aim at building 3D models of meristem development at cellular resolution based on images obtained with confocal or multiphoton microscopy. This set of components will be used by biologists and modelers making it possible to build such meristem structures, to explore and to program them. This platform is embedded in the OpenAlea framework and is based on the imaging components of the platform MedINRIA.
Partners: EPI Asclepios, RDP ENS-Lyon/INRA, PHIV CIRAD
Participants : Christophe Pradal, Christophe Godin, Michael Chelle [ INRA, EGC Grignon ] , Christian Fournier [ INRA, LEPSE ] .
Funding: INRA (Contractor for Virtual Plants: INRA, from June 2008 until December 2009)
Alinea: Building a modeling consortium around the OpenAlea platform to integrate various ecophysiological models to study interaction between the plant and its environment . The aim of this Action Ciblée Incitative of INRA is twofold. We first intend to constitute a consortium of modelers from INRA around the OpenAlea platform. Second, we aim to integrate various ecophysiological models of simulation in OpenAlea (radiative transfert, interaction between plant and pest, circulation of hydric fluxes, and dispersion). Data are provided by different teams of biologists and the integrated models will be distributed through the OpenAlea website. The project includes 3 INRA teams and the INRIA Virtual Plants team.
Participants : Frédéric Boudon, Christophe Pradal, Christophe Godin.
Funding INRIA (Contractor for Virtual Plants: INRIA. From 2009 to 2010)
M2A3PC: Modélisation de la Propagation Aérienne d'Agents Pathogènes sur une Culture Pérenne, fortement structurée et anthoprisé , the aim of this project is to model the airborne dispersal of a pathogen over a highly structured and anthropized perennial vegetal cover. This project gathers teams with different competences in biology and ecophysiology of vine and apple tree crops at different scales, 3D computer simulation of plant functioning and growth, and mathematical modeling of pest propagation in heterogenous media.
Partners: EPI Anubis (Inria Bordeaux), UMR Santé Végétale (Inra Bordeaux), EPI ALEA (Inria Bordeaux), UMR SYSTEM (INRA Montpellier), AFEF Team, UMR DAP, UMR PIAF (INRA Clermont-Ferrand), UERI de Gotheron (INRA Avignon).
Participants : Ibru Mebatsion, Frédéric Boudon, Christophe Godin, Nadia Bertin [ PSH, Avignon ] .
Funding: Agropolis fundation (Contractor for Virtual Plants: INRIA, from 2009 to 2011)
The aim of this project is to develop a virtual tomato that contains geometrical description of a growing fruit, physiological models (for sugar and hormone transfers) and mechanical model. The project gathers the competence of plant modellers, physicists and ecophysiologists. Physical and biological laws involved in tissue differentiation and cell growth, in relation to fruit growth and compartmentation, and a number of related traits of quality (e.g. size, composition and texture) are modelled and integrated within the virtual tomato. Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) techniques are used to provide an in vivo validation of the model by non invasive measurements.
Partners: PSH, INRA, Avignon; LCVN, IES, Université Sud de France, Montpellier.
Participants : Frédéric Boudon, Chakkrit Preuksakarn, Christophe Godin, Christian Fournier [ INRA, LEPSE ] .
Funding: Agropolis fundation (Contractor for Virtual Plants: CIRAD, From 2009 to 2011)
Automatic acquisition of plant phenotypes, and in particular of architecture phenotypes, constitutes a major bottleneck of the construction of quantitative models of plant development. Recently, 3D Laser Scanners (SL3D) have made it possible to acquire 3D images on which each pixel has an associated depth corresponding to distance between camera and the pinpointed surface of the object. The objective of this project is to develop the use of laser scanner for plant geometry reconstruction. For this, we will develop methodologies for the automation of numerical 3D acquisition of vegetal structures of different sizes, and develop new methods for the reconstruction of parsimonious geometrical and structural models usable in agronomical and biological contexts.
Partners: AFEF Team, UMR DAP, UMR LEPSE (Montpellier), UMR PIAF (INRA Clermont Ferrand), UMR URP3F (Inra Lusignan), EPI Galaad (INRIA Sophia Antipolis), EPI Evasion (INRIA Grenoble). University of Helsinki, Finland.
Participants : Michael Walker, Etienne Farcot Godin, Christophe Godin.
Funding: ANR (Contractor for Virtual Plants: INRIA, From 2009 to 2011)
In this project, we propose to develop a complex systems approach to study the development of multi-cellular organisms. We have chosen two distant biological systems. One is the embryo of an ascidian organism, Ciona intestinalis and the other is the female reproductive organ of a flowering plant, Arabidopsis thaliana. These two systems are very different a priori. However, there have also striking morphological similarities. Development of both systems involves the spatial control of cell growth and proliferation, while at a higher scale morphogenetic processes such as organ outgrowth or tissue invagination and folding occur. From a fundamental point of view it will, therefore, be very interesting to study how these distant organisms have solved different problems (different mechanical constrains, different number of cells, different timing) to create morphologically similar shapes.
Partners: ENS-Lyon; P. Lemaire, Luminy, Marseille.